HEADER IMMUNE SYSTEM 14-NOV-24 9KL7 TITLE CRYSTAL STRUCTURE OF A STREPTOCOCCAL PROTEIN G B1 MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN LG; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FINEGOLDIA MAGNA; SOURCE 3 ORGANISM_TAXID: 1260; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PROTEIN G B1, 3D DOMAIN-SWAPPED DIMER, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR S.SHIGA,K.MAKABE REVDAT 1 28-JAN-26 9KL7 0 JRNL AUTH S.SHIGA,H.WATANABE,K.MAKABE,S.HONDA JRNL TITL REGULATING THE ORIENTATION OF HOMOBIVALENT SMALL BINDERS JRNL TITL 2 THROUGH 3D DOMAIN-SWAPPING DESIGN. JRNL REF J.BIOL.CHEM. V. 302 11053 2025 JRNL REFN ESSN 1083-351X JRNL PMID 41391770 JRNL DOI 10.1016/J.JBC.2025.111053 REMARK 2 REMARK 2 RESOLUTION. 2.52 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 4684 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 241 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 19.1300 - 3.1700 0.99 2278 129 0.2173 0.2587 REMARK 3 2 2.6100 - 2.5200 0.98 2165 112 0.3456 0.4034 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) : 0.258 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.628 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 75.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 94.15 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 : 0.004 525 REMARK 3 ANGLE : 0.882 720 REMARK 3 CHIRALITY : 0.037 78 REMARK 3 PLANARITY : 0.006 91 REMARK 3 DIHEDRAL : 25.832 199 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 41 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.8066 5.2574 9.2582 REMARK 3 T TENSOR REMARK 3 T11: 0.9111 T22: 0.7396 REMARK 3 T33: 0.6722 T12: -0.0357 REMARK 3 T13: 0.0456 T23: -0.0486 REMARK 3 L TENSOR REMARK 3 L11: 5.8903 L22: 5.6241 REMARK 3 L33: 6.7717 L12: 0.1507 REMARK 3 L13: -1.7487 L23: -1.7851 REMARK 3 S TENSOR REMARK 3 S11: 0.1171 S12: 0.1438 S13: 0.4677 REMARK 3 S21: 0.0654 S22: -0.0049 S23: -0.2713 REMARK 3 S31: -0.4374 S32: 0.4001 S33: -0.1910 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 42 THROUGH 47 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.4882 19.5902 12.7428 REMARK 3 T TENSOR REMARK 3 T11: 1.2434 T22: 0.8255 REMARK 3 T33: 0.8480 T12: 0.0520 REMARK 3 T13: 0.0051 T23: 0.0558 REMARK 3 L TENSOR REMARK 3 L11: 2.1285 L22: 1.9631 REMARK 3 L33: 4.9126 L12: -8.2775 REMARK 3 L13: -7.5844 L23: 4.2846 REMARK 3 S TENSOR REMARK 3 S11: -0.0610 S12: 1.1476 S13: 0.8853 REMARK 3 S21: 1.7520 S22: -0.7213 S23: -0.7382 REMARK 3 S31: 2.7707 S32: 0.8059 S33: 0.8706 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 48 THROUGH 63 ) REMARK 3 ORIGIN FOR THE GROUP (A): -35.8574 34.0814 14.8008 REMARK 3 T TENSOR REMARK 3 T11: 1.0080 T22: 0.6831 REMARK 3 T33: 0.6444 T12: 0.0676 REMARK 3 T13: -0.0466 T23: -0.0259 REMARK 3 L TENSOR REMARK 3 L11: 3.8566 L22: 5.7110 REMARK 3 L33: 10.0361 L12: -0.0737 REMARK 3 L13: -3.9724 L23: 3.0340 REMARK 3 S TENSOR REMARK 3 S11: -0.6832 S12: -1.1087 S13: 0.5733 REMARK 3 S21: 0.2209 S22: 1.0365 S23: -0.1878 REMARK 3 S31: -1.2552 S32: 0.5960 S33: -0.3264 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 9KL7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1300053113. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0-8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4745 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.520 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.61 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.73700 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CONCENTRATION: 9.0 MG/ML REMARK 280 PRECIPITANTS: 1.8 M AMMONIUM SULFATE, 2% PEG 400 (HAMPTON) REMARK 280 BUFFER: 1 M HEPES-NA, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 292.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-Z+1/2 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 23.26950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.57100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.62400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.57100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.26950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.62400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 23.26950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.62400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 42.57100 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.62400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 23.26950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 42.57100 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: 2970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -46.53900 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 33.62400 REMARK 350 BIOMT3 2 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 -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 DBREF 9KL7 A 1 63 UNP Q53291 Q53291_FINMA 328 384 SEQADV 9KL7 GLY A -2 UNP Q53291 EXPRESSION TAG SEQADV 9KL7 SER A -1 UNP Q53291 EXPRESSION TAG SEQADV 9KL7 HIS A 0 UNP Q53291 EXPRESSION TAG SEQADV 9KL7 GLU A 37 UNP Q53291 ASP 364 ENGINEERED MUTATION SEQADV 9KL7 HIS A 38 UNP Q53291 ASN 365 ENGINEERED MUTATION SEQADV 9KL7 PRO A 42 UNP Q53291 INSERTION SEQADV 9KL7 PRO A 43 UNP Q53291 INSERTION SEQADV 9KL7 PRO A 44 UNP Q53291 INSERTION SEQADV 9KL7 PRO A 45 UNP Q53291 INSERTION SEQADV 9KL7 PRO A 46 UNP Q53291 INSERTION SEQADV 9KL7 PRO A 47 UNP Q53291 INSERTION SEQADV 9KL7 PRO A 54 UNP Q53291 ASP 375 ENGINEERED MUTATION SEQADV 9KL7 GLU A 55 UNP Q53291 ALA 376 ENGINEERED MUTATION SEQRES 1 A 66 GLY SER HIS MET ASP THR TYR LYS LEU ILE LEU ASN GLY SEQRES 2 A 66 LYS THR LEU LYS GLY GLU THR THR THR GLU ALA VAL ASP SEQRES 3 A 66 ALA ALA THR ALA GLU LYS VAL PHE LYS GLN TYR ALA ASN SEQRES 4 A 66 GLU HIS GLY VAL ASP PRO PRO PRO PRO PRO PRO GLY GLU SEQRES 5 A 66 TRP THR TYR ASP PRO GLU THR LYS THR PHE THR VAL THR SEQRES 6 A 66 GLU HET EPE A 101 15 HET SO4 A 102 5 HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM SO4 SULFATE ION HETSYN EPE HEPES FORMUL 2 EPE C8 H18 N2 O4 S FORMUL 3 SO4 O4 S 2- HELIX 1 AA1 ASP A 23 HIS A 38 1 16 SHEET 1 AA1 2 ASP A 2 ASN A 9 0 SHEET 2 AA1 2 LYS A 14 ALA A 21 -1 O THR A 17 N LEU A 6 SHEET 1 AA2 2 GLU A 49 ASP A 53 0 SHEET 2 AA2 2 THR A 58 THR A 62 -1 O THR A 62 N GLU A 49 CRYST1 46.539 67.248 85.142 90.00 90.00 90.00 I 21 21 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 0.021487 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014870 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011745 0.00000 CONECT 494 495 499 503 CONECT 495 494 496 CONECT 496 495 497 CONECT 497 496 498 500 CONECT 498 497 499 CONECT 499 494 498 CONECT 500 497 501 CONECT 501 500 502 CONECT 502 501 CONECT 503 494 504 CONECT 504 503 505 CONECT 505 504 506 507 508 CONECT 506 505 CONECT 507 505 CONECT 508 505 CONECT 509 510 511 512 513 CONECT 510 509 CONECT 511 509 CONECT 512 509 CONECT 513 509 MASTER 269 0 2 1 4 0 0 6 512 1 20 6 END