HEADER IMMUNE SYSTEM 07-MAR-25 9M6J TITLE CRYSTAL STRUCTURE OF S. AUREUS PROTEIN A BOUND TO A CAMELID SINGLE- TITLE 2 DOMAIN ANTIBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: SINGLE-DOMAIN ANTIBODY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: IMMUNOGLOBULIN G-BINDING PROTEIN A; COMPND 7 CHAIN: H; COMPND 8 SYNONYM: IGG-BINDING PROTEIN A,STAPHYLOCOCCAL PROTEIN A,SPA; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAMELIDAE; SOURCE 3 ORGANISM_TAXID: 9835; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325; SOURCE 8 ORGANISM_TAXID: 93061; SOURCE 9 GENE: SPA, SAOUHSC_00069; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR Y.KONG,J.L.SHI,F.D.WU,T.ZHAO,X.Y.ZHU,Q.Y.XU,R.B.WANG,Y.D.SONG,Q.X.LI, AUTHOR 2 Y.L.WANG,X.Y.GAO,Y.D.YANG,Y.L.WU,Z.L.YANG,J.H.YAO,T.L.YING REVDAT 1 12-NOV-25 9M6J 0 JRNL AUTH Y.KONG,J.SHI,F.WU,T.ZHAO,R.WANG,X.ZHU,Q.XU,Y.SONG,Q.LI, JRNL AUTH 2 Y.WANG,X.GAO,Y.YANG,Y.FENG,Z.WANG,W.GE,Y.WU,Z.YANG,J.YAO, JRNL AUTH 3 T.YING JRNL TITL A SYNERGISTIC GENERATIVE-RANKING FRAMEWORK FOR TAILORED JRNL TITL 2 DESIGN OF THERAPEUTIC SINGLE-DOMAIN ANTIBODIES. JRNL REF CELL DISCOV V. 11 85 2025 JRNL REFN ESSN 2056-5968 JRNL PMID 41162386 JRNL DOI 10.1038/S41421-025-00843-8 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 13892 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.690 REMARK 3 FREE R VALUE TEST SET COUNT : 652 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 25.3100 - 3.4200 0.99 2796 121 0.1826 0.2152 REMARK 3 2 3.4200 - 2.7100 0.99 2649 143 0.2011 0.2384 REMARK 3 3 2.7100 - 2.3700 0.99 2644 135 0.2004 0.2371 REMARK 3 4 2.3700 - 2.1500 0.98 2594 126 0.1926 0.2171 REMARK 3 5 2.1500 - 2.0000 0.97 2557 127 0.1952 0.2187 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) : 0.181 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.581 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.18 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 : 0.006 1413 REMARK 3 ANGLE : 0.773 1911 REMARK 3 CHIRALITY : 0.055 202 REMARK 3 PLANARITY : 0.006 253 REMARK 3 DIHEDRAL : 14.768 516 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 14.3202 16.5018 5.5587 REMARK 3 T TENSOR REMARK 3 T11: 0.1191 T22: 0.0974 REMARK 3 T33: 0.0761 T12: -0.0035 REMARK 3 T13: 0.0179 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 3.3271 L22: 1.5346 REMARK 3 L33: 1.0593 L12: -0.7580 REMARK 3 L13: 0.1030 L23: 0.2800 REMARK 3 S TENSOR REMARK 3 S11: -0.0163 S12: -0.0521 S13: -0.0177 REMARK 3 S21: 0.0037 S22: 0.0387 S23: -0.0678 REMARK 3 S31: -0.0365 S32: 0.0551 S33: -0.0197 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 9M6J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 11-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1300057270. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-24 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 : SSRF REMARK 200 BEAMLINE : BL10U2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13903 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 61.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.11700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.18.2_3874 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M AMMONIUM SULFATE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.32500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.32500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 39.29000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.06000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 39.29000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.06000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 26.32500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 39.29000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.06000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 26.32500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 39.29000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.06000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H 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 GLN A 1 REMARK 465 ALA H 2796 REMARK 465 ASP H 2797 REMARK 465 ALA H 2798 REMARK 465 GLN H 2799 REMARK 465 GLN H 2800 REMARK 465 ASN H 2801 REMARK 465 ASN H 2802 REMARK 465 PHE H 2803 REMARK 465 ASN H 2804 DBREF 9M6J A 1 127 PDB 9M6J 9M6J 1 127 DBREF 9M6J H 2796 2856 UNP P02976 SPA_STAA8 93 153 SEQRES 1 A 127 GLN VAL GLN LEU GLN ASP SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 127 ALA GLY GLY SER LEU ARG LEU SER CYS ALA VAL SER GLY SEQRES 3 A 127 ARG THR PHE SER ALA HIS SER VAL TYR THR MET GLY TRP SEQRES 4 A 127 PHE ARG GLN ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA SEQRES 5 A 127 ARG ILE TYR TRP SER SER ALA ASN THR TYR TYR ALA ASP SEQRES 6 A 127 SER VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA SEQRES 7 A 127 LYS ASN THR VAL TYR LEU GLN MET ASN SER LEU ARG PRO SEQRES 8 A 127 GLU ASP THR ALA VAL TYR TYR CYS ALA ALA ARG ASP GLY SEQRES 9 A 127 ILE PRO THR SER ARG THR VAL GLY SER TYR ASN TYR TRP SEQRES 10 A 127 GLY GLN GLY THR GLN VAL THR VAL SER SER SEQRES 1 H 61 ALA ASP ALA GLN GLN ASN ASN PHE ASN LYS ASP GLN GLN SEQRES 2 H 61 SER ALA PHE TYR GLU ILE LEU ASN MET PRO ASN LEU ASN SEQRES 3 H 61 GLU ALA GLN ARG ASN GLY PHE ILE GLN SER LEU LYS ASP SEQRES 4 H 61 ASP PRO SER GLN SER THR ASN VAL LEU GLY GLU ALA LYS SEQRES 5 H 61 LYS LEU ASN GLU SER GLN ALA PRO LYS FORMUL 3 HOH *153(H2 O) HELIX 1 AA1 ASP A 65 LYS A 68 5 4 HELIX 2 AA2 ARG A 90 THR A 94 5 5 HELIX 3 AA3 THR A 110 TYR A 114 5 5 HELIX 4 AA4 ASP H 2806 MET H 2817 1 12 HELIX 5 AA5 ASN H 2821 ASP H 2835 1 15 HELIX 6 AA6 GLN H 2838 GLN H 2853 1 16 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -1 O SER A 25 N GLN A 3 SHEET 3 AA1 4 THR A 81 MET A 86 -1 O MET A 86 N LEU A 18 SHEET 4 AA1 4 PHE A 71 ASP A 76 -1 N SER A 74 O TYR A 83 SHEET 1 AA2 6 LEU A 11 GLN A 13 0 SHEET 2 AA2 6 THR A 121 SER A 126 1 O THR A 124 N VAL A 12 SHEET 3 AA2 6 ALA A 95 ARG A 102 -1 N TYR A 97 O THR A 121 SHEET 4 AA2 6 THR A 36 GLN A 42 -1 N PHE A 40 O TYR A 98 SHEET 5 AA2 6 ARG A 48 TYR A 55 -1 O ILE A 54 N MET A 37 SHEET 6 AA2 6 THR A 61 TYR A 63 -1 O TYR A 62 N ARG A 53 SHEET 1 AA3 4 LEU A 11 GLN A 13 0 SHEET 2 AA3 4 THR A 121 SER A 126 1 O THR A 124 N VAL A 12 SHEET 3 AA3 4 ALA A 95 ARG A 102 -1 N TYR A 97 O THR A 121 SHEET 4 AA3 4 TYR A 116 TRP A 117 -1 O TYR A 116 N ALA A 101 SSBOND 1 CYS A 22 CYS A 99 1555 1555 2.04 CRYST1 78.580 98.120 52.650 90.00 90.00 90.00 C 2 2 21 8 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 0.012726 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010192 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018993 0.00000