HEADER IMMUNE SYSTEM 26-MAR-24 8YTP TITLE SINGLE-CHAIN FV ANTIBODY OF E11 COMPLEX WITH NP-GLYCINE UNDER REDUCING TITLE 2 CONDITIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SINGLE-CHAIN FV ANTIBODY OF E11; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ANTIGEN BINDING, AFFINITY MATURATION, SOMATIC HYPERMUTATION, IMMUNE KEYWDS 2 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR M.YOSHIDA,Y.HANAZONO,N.NUMOTO,N.ITO,M.ODA JRNL AUTH M.YOSHIDA,Y.HANAZONO,N.NUMOTO,S.NAGAO,S.YABUNO,Y.KITAGAWA, JRNL AUTH 2 H.SEKIGUCHI,N.ITO,T.AZUMA,M.ODA JRNL TITL AFFINITY-MATURED ANTIBODY WITH A DISULFIDE BOND IN H-CDR3 JRNL TITL 2 LOOP. JRNL REF ARCH.BIOCHEM.BIOPHYS. 10068 2024 JRNL REFN ESSN 1096-0384 JRNL PMID 38909835 JRNL DOI 10.1016/J.ABB.2024.110068 REMARK 2 REMARK 2 RESOLUTION. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 42161 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2109 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 35.9900 - 3.3500 0.96 2804 148 0.1379 0.1479 REMARK 3 2 3.3500 - 2.6600 0.99 2742 145 0.1499 0.1720 REMARK 3 3 2.6600 - 2.3300 0.98 2685 141 0.1490 0.1545 REMARK 3 4 2.3300 - 2.1100 1.00 2709 143 0.1324 0.1665 REMARK 3 5 2.1100 - 1.9600 0.99 2689 141 0.1306 0.1764 REMARK 3 6 1.9600 - 1.8500 0.99 2696 142 0.1360 0.1742 REMARK 3 7 1.8500 - 1.7500 0.99 2672 141 0.1303 0.1927 REMARK 3 8 1.7500 - 1.6800 0.99 2638 139 0.1380 0.2080 REMARK 3 9 1.6800 - 1.6100 0.99 2663 140 0.1525 0.1902 REMARK 3 10 1.6100 - 1.5600 1.00 2670 140 0.1591 0.2187 REMARK 3 11 1.5600 - 1.5100 0.98 2642 140 0.1642 0.2164 REMARK 3 12 1.5100 - 1.4700 0.98 2624 137 0.1805 0.2423 REMARK 3 13 1.4600 - 1.4300 1.00 2632 139 0.1982 0.2535 REMARK 3 14 1.4300 - 1.3900 0.98 2615 137 0.2219 0.2588 REMARK 3 15 1.3900 - 1.3600 0.96 2571 136 0.2380 0.2917 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.640 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 : 0.012 1944 REMARK 3 ANGLE : 1.256 2668 REMARK 3 CHIRALITY : 0.113 292 REMARK 3 PLANARITY : 0.009 345 REMARK 3 DIHEDRAL : 15.299 700 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 8YTP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ. REMARK 100 THE DEPOSITION ID IS D_1300046352. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-23 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 : SPRING-8 REMARK 200 BEAMLINE : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42209 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.00400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 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: 6K4Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES SODIUM PH 7.5, 10% V/V 2 REMARK 280 -PROPANOL, 20% W/V POLYETHYLENE GLYCOL 4000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 17.84000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.41000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.71000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.41000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.84000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.71000 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A 1 REMARK 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 GLN A 4 REMARK 465 GLY A 121 REMARK 465 GLY A 122 REMARK 465 GLY A 123 REMARK 465 SER A 124 REMARK 465 GLY A 125 REMARK 465 GLY A 126 REMARK 465 GLY A 127 REMARK 465 GLY A 128 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 ASP A 46 42.81 70.06 REMARK 500 HIS A 47 59.46 27.45 REMARK 500 HIS A 47 59.14 27.64 REMARK 500 ASN A 56 -46.63 76.41 REMARK 500 TYR A 97 64.33 -116.95 REMARK 500 SER A 98 -41.51 76.34 REMARK 500 ASN A 99 10.01 -146.45 REMARK 500 CYS A 229 133.70 -171.12 REMARK 500 CYS A 232 -150.94 -119.82 REMARK 500 PHE A 235 30.82 70.36 REMARK 500 REMARK 500 REMARK: NULL DBREF 8YTP A 1 248 PDB 8YTP 8YTP 1 248 SEQRES 1 A 248 GLY SER ALA GLN ALA VAL VAL THR GLN GLU SER ALA LEU SEQRES 2 A 248 THR THR SER PRO GLY GLU THR VAL THR LEU THR CYS ARG SEQRES 3 A 248 SER SER THR GLY ALA VAL ILE SER SER ASN PHE VAL SER SEQRES 4 A 248 TRP VAL GLN GLU LYS PRO ASP HIS LEU PHE THR GLY LEU SEQRES 5 A 248 ILE GLY GLY ASN LYS ASN ARG ALA PRO GLY VAL PRO ALA SEQRES 6 A 248 ARG PHE SER GLY SER LEU ILE GLY ASP LYS ALA VAL LEU SEQRES 7 A 248 THR ILE THR GLY ALA GLN THR GLU ASP GLU ALA ILE TYR SEQRES 8 A 248 PHE CYS ALA LEU TRP TYR SER ASN HIS TRP VAL PHE GLY SEQRES 9 A 248 GLY GLY THR LYS LEU THR VAL LEU GLY GLN GLY GLY GLY SEQRES 10 A 248 GLY SER GLY GLY GLY GLY SER GLY GLY GLY GLY SER GLN SEQRES 11 A 248 VAL GLN LEU GLN GLN PRO GLY ALA GLU LEU ALA LYS PRO SEQRES 12 A 248 GLY ALA SER VAL GLN LEU SER CYS LYS GLY SER GLY TYR SEQRES 13 A 248 THR PHE PRO ASN TYR TRP MET HIS TRP VAL THR GLN ARG SEQRES 14 A 248 PRO GLY ARG GLY LEU GLU TRP ILE GLY ARG ILE ASP PRO SEQRES 15 A 248 ASN SER GLY PHE ILE ARG TYR ASP GLU ARG PHE LYS THR SEQRES 16 A 248 LYS ALA THR LEU THR VAL ASP LYS PRO SER SER THR ALA SEQRES 17 A 248 TYR MET GLN LEU SER SER LEU THR SER ASP ASP SER ALA SEQRES 18 A 248 VAL TYR PHE CYS ALA ARG GLY CYS TYR GLY CYS ILE HIS SEQRES 19 A 248 PHE ASP TYR TRP GLY GLN GLY THR THR LEU THR VAL SER SEQRES 20 A 248 SER HET LZO A 401 18 FORMUL 2 LZO FORMUL 3 HOH *222(H2 O) HELIX 1 AA1 ILE A 33 PHE A 37 5 5 HELIX 2 AA2 GLN A 84 GLU A 88 5 5 HELIX 3 AA3 THR A 157 TYR A 161 5 5 HELIX 4 AA4 GLU A 191 LYS A 194 5 4 HELIX 5 AA5 THR A 216 SER A 220 5 5 SHEET 1 AA1 4 VAL A 7 GLN A 9 0 SHEET 2 AA1 4 THR A 20 SER A 27 -1 O ARG A 26 N THR A 8 SHEET 3 AA1 4 LYS A 75 THR A 81 -1 O ILE A 80 N VAL A 21 SHEET 4 AA1 4 PHE A 67 ILE A 72 -1 N SER A 68 O THR A 79 SHEET 1 AA2 6 ALA A 12 THR A 15 0 SHEET 2 AA2 6 THR A 107 VAL A 111 1 O THR A 110 N THR A 15 SHEET 3 AA2 6 ALA A 89 TRP A 96 -1 N ALA A 89 O LEU A 109 SHEET 4 AA2 6 SER A 39 LYS A 44 -1 N GLU A 43 O ILE A 90 SHEET 5 AA2 6 LEU A 48 GLY A 54 -1 O LEU A 52 N TRP A 40 SHEET 6 AA2 6 ASN A 58 ARG A 59 -1 O ASN A 58 N GLY A 54 SHEET 1 AA3 4 ALA A 12 THR A 15 0 SHEET 2 AA3 4 THR A 107 VAL A 111 1 O THR A 110 N THR A 15 SHEET 3 AA3 4 ALA A 89 TRP A 96 -1 N ALA A 89 O LEU A 109 SHEET 4 AA3 4 TRP A 101 PHE A 103 -1 O VAL A 102 N LEU A 95 SHEET 1 AA4 4 GLN A 132 GLN A 134 0 SHEET 2 AA4 4 VAL A 147 SER A 154 -1 O LYS A 152 N GLN A 134 SHEET 3 AA4 4 THR A 207 LEU A 212 -1 O MET A 210 N LEU A 149 SHEET 4 AA4 4 ALA A 197 ASP A 202 -1 N ASP A 202 O THR A 207 SHEET 1 AA5 6 ALA A 138 ALA A 141 0 SHEET 2 AA5 6 THR A 242 VAL A 246 1 O THR A 245 N GLU A 139 SHEET 3 AA5 6 ALA A 221 GLY A 228 -1 N ALA A 221 O LEU A 244 SHEET 4 AA5 6 TRP A 162 ARG A 169 -1 N HIS A 164 O ALA A 226 SHEET 5 AA5 6 GLY A 173 ILE A 180 -1 O ILE A 177 N TRP A 165 SHEET 6 AA5 6 ILE A 187 TYR A 189 -1 O ARG A 188 N ARG A 179 SSBOND 1 CYS A 25 CYS A 93 1555 1555 2.05 SSBOND 2 CYS A 151 CYS A 225 1555 1555 2.04 CRYST1 35.680 61.420 88.820 90.00 90.00 90.00 P 21 21 21 4 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 0.028027 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016281 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011259 0.00000