HEADER IMMUNE SYSTEM 13-JAN-25 9HZK TITLE SDAB9 IN COMPLEX WITH PFCSP ATSR DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CIRCUMSPOROZOITE PROTEIN; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: CS,PFCSP; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: SDAB9; COMPND 8 CHAIN: A; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM NF54; SOURCE 3 ORGANISM_TAXID: 5843; SOURCE 4 GENE: CSP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 9 ORGANISM_TAXID: 9844; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MALARIA, CIRCUMSPOROZOITE PROTEIN, CAMELID SINGLE-DOMAIN ANTIBODY, KEYWDS 2 IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR Y.G.-J.STERCKX,R.GEENS REVDAT 1 23-APR-25 9HZK 0 JRNL AUTH R.GEENS,L.DE VOCHT,M.C.AGUIRRE-BOTERO,C.VINCKE,E.ROMAO, JRNL AUTH 2 S.MAGEZ,S.MUYLDERMANS,R.AMINO,Y.G.-J.STERCKX JRNL TITL EVIDENCE FOR A MODEL OF CONFORMATIONAL CHANGE BY THE JRNL TITL 2 PLASMODIUM FALCIPARUM CIRCUMSPOROZOITE PROTEIN DURING JRNL TITL 3 SPOROZOITE DEVELOPMENT IN THE MOSQUITO HOST THROUGH THE USE JRNL TITL 4 OF CAMELID SINGLE-DOMAIN ANTIBODIES JRNL REF TO BE PUBLISHED JRNL REFN JRNL DOI 10.1128/IAI.00081-25 REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21.2_5419: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 11856 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 592 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 25.4600 - 3.2900 0.99 2810 147 0.1423 0.1719 REMARK 3 2 3.2900 - 2.6100 1.00 2810 148 0.1837 0.2524 REMARK 3 3 2.6100 - 2.2800 1.00 2832 149 0.2418 0.3162 REMARK 3 4 2.2800 - 2.0700 1.00 2812 148 0.3760 0.3945 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1570 REMARK 3 ANGLE : 0.855 2091 REMARK 3 CHIRALITY : 0.050 214 REMARK 3 PLANARITY : 0.009 265 REMARK 3 DIHEDRAL : 15.034 585 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9HZK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1292144626. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.967697 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23186 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 REMARK 200 RESOLUTION RANGE LOW (A) : 25.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.3600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.680 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% PEG4000, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.56000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.28000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET B 309 REMARK 465 VAL B 377 REMARK 465 PHE B 378 REMARK 465 ASN B 379 REMARK 465 VAL B 380 REMARK 465 VAL B 381 REMARK 465 ASN B 382 REMARK 465 SER B 383 REMARK 465 SER B 384 REMARK 465 GLU B 385 REMARK 465 ASN B 386 REMARK 465 LEU B 387 REMARK 465 TYR B 388 REMARK 465 PHE B 389 REMARK 465 GLN B 390 REMARK 465 SER B 391 REMARK 465 GLY B 392 REMARK 465 GLY B 393 REMARK 465 HIS B 394 REMARK 465 HIS B 395 REMARK 465 HIS B 396 REMARK 465 HIS B 397 REMARK 465 HIS B 398 REMARK 465 HIS B 399 REMARK 465 ALA A 126 REMARK 465 ALA A 127 REMARK 465 ALA A 128 REMARK 465 TYR A 129 REMARK 465 PRO A 130 REMARK 465 TYR A 131 REMARK 465 ASP A 132 REMARK 465 VAL A 133 REMARK 465 PRO A 134 REMARK 465 ASP A 135 REMARK 465 TYR A 136 REMARK 465 GLY A 137 REMARK 465 SER A 138 REMARK 465 HIS A 139 REMARK 465 HIS A 140 REMARK 465 HIS A 141 REMARK 465 HIS A 142 REMARK 465 HIS A 143 REMARK 465 HIS A 144 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 1 CG CD OE1 NE2 REMARK 470 ARG A 27 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU B 372 154.47 -48.99 REMARK 500 ASN A 106 111.02 -162.28 REMARK 500 REMARK 500 REMARK: NULL DBREF 9HZK B 310 384 UNP P19597 CSP_PLAFO 310 384 DBREF 9HZK A 1 144 PDB 9HZK 9HZK 1 144 SEQADV 9HZK MET B 309 UNP P19597 INITIATING METHIONINE SEQADV 9HZK GLU B 385 UNP P19597 EXPRESSION TAG SEQADV 9HZK ASN B 386 UNP P19597 EXPRESSION TAG SEQADV 9HZK LEU B 387 UNP P19597 EXPRESSION TAG SEQADV 9HZK TYR B 388 UNP P19597 EXPRESSION TAG SEQADV 9HZK PHE B 389 UNP P19597 EXPRESSION TAG SEQADV 9HZK GLN B 390 UNP P19597 EXPRESSION TAG SEQADV 9HZK SER B 391 UNP P19597 EXPRESSION TAG SEQADV 9HZK GLY B 392 UNP P19597 EXPRESSION TAG SEQADV 9HZK GLY B 393 UNP P19597 EXPRESSION TAG SEQADV 9HZK HIS B 394 UNP P19597 EXPRESSION TAG SEQADV 9HZK HIS B 395 UNP P19597 EXPRESSION TAG SEQADV 9HZK HIS B 396 UNP P19597 EXPRESSION TAG SEQADV 9HZK HIS B 397 UNP P19597 EXPRESSION TAG SEQADV 9HZK HIS B 398 UNP P19597 EXPRESSION TAG SEQADV 9HZK HIS B 399 UNP P19597 EXPRESSION TAG SEQRES 1 B 91 MET GLU PRO SER ASP LYS HIS ILE LYS GLU TYR LEU ASN SEQRES 2 B 91 LYS ILE GLN ASN SER LEU SER THR GLU TRP SER PRO CYS SEQRES 3 B 91 SER VAL THR CYS GLY ASN GLY ILE GLN VAL ARG ILE LYS SEQRES 4 B 91 PRO GLY SER ALA ASN LYS PRO LYS ASP GLU LEU ASP TYR SEQRES 5 B 91 ALA ASN ASP ILE GLU LYS LYS ILE CYS LYS MET GLU LYS SEQRES 6 B 91 CYS SER SER VAL PHE ASN VAL VAL ASN SER SER GLU ASN SEQRES 7 B 91 LEU TYR PHE GLN SER GLY GLY HIS HIS HIS HIS HIS HIS SEQRES 1 A 144 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 144 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 144 ARG THR PHE SER SER TYR SER MET GLY TRP PHE ARG GLN SEQRES 4 A 144 VAL PRO GLY LYS GLU ARG GLU PHE VAL ALA ARG ILE THR SEQRES 5 A 144 SER SER GLY GLY ASN THR ASP TYR ALA ASP SER ALA LYS SEQRES 6 A 144 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 A 144 VAL TYR LEU GLN MET SER THR LEU LYS PRO GLU ASP THR SEQRES 8 A 144 ALA VAL TYR TYR CYS ALA ALA ASP LEU TRP GLN TYR GLY SEQRES 9 A 144 ARG ASN SER ARG ALA ALA ASP TYR ASP TYR TRP GLY GLN SEQRES 10 A 144 GLY THR GLN VAL THR VAL SER SER ALA ALA ALA TYR PRO SEQRES 11 A 144 TYR ASP VAL PRO ASP TYR GLY SER HIS HIS HIS HIS HIS SEQRES 12 A 144 HIS HET GOL B 401 6 HET GOL B 402 6 HET GOL B 403 6 HET GOL B 404 6 HET GOL B 405 6 HET PEG A 201 7 HET GOL A 202 6 HET PEG A 203 7 HET GOL A 204 6 HET GOL A 205 6 HET GOL A 206 6 HET PEG A 207 7 HET GOL A 208 6 HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 10(C3 H8 O3) FORMUL 8 PEG 3(C4 H10 O3) FORMUL 16 HOH *86(H2 O) HELIX 1 AA1 SER B 312 ILE B 323 1 12 HELIX 2 AA2 GLN B 324 LEU B 327 5 4 HELIX 3 AA3 PRO B 348 ALA B 351 5 4 HELIX 4 AA4 PRO B 354 LEU B 358 5 5 HELIX 5 AA5 THR A 28 TYR A 32 5 5 HELIX 6 AA6 LYS A 87 THR A 91 5 5 HELIX 7 AA7 ARG A 108 TYR A 112 5 5 SHEET 1 AA1 2 ASN B 340 ILE B 346 0 SHEET 2 AA1 2 ILE B 364 LYS B 370 -1 O CYS B 369 N GLY B 341 SHEET 1 AA2 4 LEU A 4 SER A 7 0 SHEET 2 AA2 4 LEU A 18 ALA A 24 -1 O SER A 21 N SER A 7 SHEET 3 AA2 4 THR A 78 MET A 83 -1 O MET A 83 N LEU A 18 SHEET 4 AA2 4 THR A 69 ASP A 73 -1 N SER A 71 O TYR A 80 SHEET 1 AA3 6 LEU A 11 GLN A 13 0 SHEET 2 AA3 6 THR A 119 SER A 124 1 O THR A 122 N VAL A 12 SHEET 3 AA3 6 ALA A 92 ASP A 99 -1 N ALA A 92 O VAL A 121 SHEET 4 AA3 6 SER A 33 GLN A 39 -1 N SER A 33 O ASP A 99 SHEET 5 AA3 6 GLU A 46 ILE A 51 -1 O GLU A 46 N ARG A 38 SHEET 6 AA3 6 THR A 58 TYR A 60 -1 O ASP A 59 N ARG A 50 SHEET 1 AA4 4 LEU A 11 GLN A 13 0 SHEET 2 AA4 4 THR A 119 SER A 124 1 O THR A 122 N VAL A 12 SHEET 3 AA4 4 ALA A 92 ASP A 99 -1 N ALA A 92 O VAL A 121 SHEET 4 AA4 4 TYR A 114 TRP A 115 -1 O TYR A 114 N ALA A 98 SSBOND 1 CYS B 334 CYS B 369 1555 1555 2.04 SSBOND 2 CYS B 338 CYS B 374 1555 1555 2.05 SSBOND 3 CYS A 22 CYS A 96 1555 1555 2.03 CRYST1 53.740 53.740 60.840 90.00 90.00 120.00 P 32 3 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.018608 0.010743 0.000000 0.00000 SCALE2 0.000000 0.021487 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016437 0.00000