HEADER IMMUNE SYSTEM 13-NOV-25 9T8Z TITLE ROOM TEMPERATURE X-RAY STRUCTURE OF THE B1 DOMAIN OF STREPTOCOCCAL TITLE 2 PROTEIN G TRIPLE MUTANT T2Q, N8D, AND N37D (GB1-QDD). COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMMUNOGLOBULIN G-BINDING PROTEIN G; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: IGG-BINDING PROTEIN G; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS SP.; SOURCE 3 ORGANISM_TAXID: 1306; SOURCE 4 GENE: SPG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS B1 DOMAIN, TRIPLE MUTANT, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR S.ENGILBERGE,L.M.BECKER,A.KAPITONOVA,P.SCHANDA REVDAT 1 04-MAR-26 9T8Z 0 JRNL AUTH L.M.BECKER,H.FU,B.P.TATMAN,M.DREYDOPPEL,A.KAPITONOVA, JRNL AUTH 2 U.WEININGER,S.ENGILBERGE,C.CHIPOT,P.SCHANDA JRNL TITL AROMATIC RING FLIPS REVEAL RESHAPING OF PROTEIN DYNAMICS IN JRNL TITL 2 CRYSTALS AND COMPLEXES JRNL REF BIORXIV 2025 JRNL REFN ISSN 2692-8205 JRNL DOI 10.1101/2025.08.20.671406 REMARK 2 REMARK 2 RESOLUTION. 1.69 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) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 13157 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 675 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 31.2300 - 2.8900 1.00 2624 151 0.1491 0.1717 REMARK 3 2 2.8900 - 2.3000 1.00 2595 144 0.1862 0.2175 REMARK 3 3 2.3000 - 2.0100 1.00 2570 136 0.1692 0.2202 REMARK 3 4 2.0100 - 1.8200 0.98 2514 128 0.1729 0.2121 REMARK 3 5 1.8200 - 1.6900 0.85 2179 116 0.2002 0.2413 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) : 0.193 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.129 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.46 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 : 0.013 912 REMARK 3 ANGLE : 1.235 1241 REMARK 3 CHIRALITY : 0.076 144 REMARK 3 PLANARITY : 0.008 158 REMARK 3 DIHEDRAL : 13.939 329 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND ( RESID 1:56 OR RESID 202:234 OR RESID REMARK 3 101:101 ) ) OR ( CHAIN B AND ( RESID 1:56 OR RESID REMARK 3 102:138 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.680 -9.844 11.879 REMARK 3 T TENSOR REMARK 3 T11: 0.1269 T22: 0.1262 REMARK 3 T33: 0.1304 T12: 0.0094 REMARK 3 T13: -0.0049 T23: 0.0060 REMARK 3 L TENSOR REMARK 3 L11: 0.8231 L22: 1.9013 REMARK 3 L33: 0.7906 L12: 1.6082 REMARK 3 L13: 0.8645 L23: 1.4777 REMARK 3 S TENSOR REMARK 3 S11: -0.0191 S12: -0.0001 S13: -0.0334 REMARK 3 S21: -0.0415 S22: 0.0158 S23: -0.0036 REMARK 3 S31: -0.0218 S32: -0.0153 S33: 0.0060 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 9T8Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-NOV-25. REMARK 100 THE DEPOSITION ID IS D_1292151997. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-25 REMARK 200 TEMPERATURE (KELVIN) : 295 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) : 0.95372 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X CDTE 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13158 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 31.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.700 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 (%): 49.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 % 2-METHYL-2,4-PENTANEDIOL (MPD), REMARK 280 25 % ISOPROPANOL, MICRODIALYSIS, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 39.34950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.70450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 39.34950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.70450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 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 2 CG CD OE1 NE2 REMARK 470 ASN B 35 CG OD1 ND2 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 8 70.72 -119.23 REMARK 500 ASP B 8 67.95 -115.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 252 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH B 145 DISTANCE = 6.08 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 19 OE1 REMARK 620 2 HOH A 233 O 119.7 REMARK 620 3 THR B 17 OG1 111.0 9.6 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9I2I RELATED DB: PDB DBREF 9T8Z A 2 56 UNP P19909 SPG2_STRSG 303 357 DBREF 9T8Z B 2 56 UNP P19909 SPG2_STRSG 303 357 SEQADV 9T8Z MET A 1 UNP P19909 INITIATING METHIONINE SEQADV 9T8Z GLN A 2 UNP P19909 THR 303 ENGINEERED MUTATION SEQADV 9T8Z ASP A 8 UNP P19909 ASN 309 ENGINEERED MUTATION SEQADV 9T8Z ASP A 37 UNP P19909 ASN 338 ENGINEERED MUTATION SEQADV 9T8Z MET B 1 UNP P19909 INITIATING METHIONINE SEQADV 9T8Z GLN B 2 UNP P19909 THR 303 ENGINEERED MUTATION SEQADV 9T8Z ASP B 8 UNP P19909 ASN 309 ENGINEERED MUTATION SEQADV 9T8Z ASP B 37 UNP P19909 ASN 338 ENGINEERED MUTATION SEQRES 1 A 56 MET GLN TYR LYS LEU ILE LEU ASP GLY LYS THR LEU LYS SEQRES 2 A 56 GLY GLU THR THR THR GLU ALA VAL ASP ALA ALA THR ALA SEQRES 3 A 56 GLU LYS VAL PHE LYS GLN TYR ALA ASN ASP ASP GLY VAL SEQRES 4 A 56 ASP GLY GLU TRP THR TYR ASP ASP ALA THR LYS THR PHE SEQRES 5 A 56 THR VAL THR GLU SEQRES 1 B 56 MET GLN TYR LYS LEU ILE LEU ASP GLY LYS THR LEU LYS SEQRES 2 B 56 GLY GLU THR THR THR GLU ALA VAL ASP ALA ALA THR ALA SEQRES 3 B 56 GLU LYS VAL PHE LYS GLN TYR ALA ASN ASP ASP GLY VAL SEQRES 4 B 56 ASP GLY GLU TRP THR TYR ASP ASP ALA THR LYS THR PHE SEQRES 5 B 56 THR VAL THR GLU HET NA A 101 1 HETNAM NA SODIUM ION FORMUL 3 NA NA 1+ FORMUL 4 HOH *97(H2 O) HELIX 1 AA1 ASP A 22 ASP A 37 1 16 HELIX 2 AA2 ASP B 22 ASP B 37 1 16 SHEET 1 AA1 8 GLU A 42 ASP A 46 0 SHEET 2 AA1 8 THR A 51 THR A 55 -1 O THR A 55 N GLU A 42 SHEET 3 AA1 8 GLN A 2 ASP A 8 1 N LYS A 4 O PHE A 52 SHEET 4 AA1 8 LEU A 12 GLU A 19 -1 O THR A 16 N LEU A 5 SHEET 5 AA1 8 LEU B 12 GLU B 19 -1 O LYS B 13 N LYS A 13 SHEET 6 AA1 8 GLN B 2 ASP B 8 -1 N LEU B 5 O THR B 16 SHEET 7 AA1 8 THR B 51 THR B 55 1 O PHE B 52 N LYS B 4 SHEET 8 AA1 8 GLU B 42 ASP B 46 -1 N GLU B 42 O THR B 55 LINK OE1 GLU A 19 NA NA A 101 1555 1555 2.60 LINK NA NA A 101 O HOH A 233 1555 1555 2.64 LINK NA NA A 101 OG1 THR B 17 1545 1555 2.93 CRYST1 78.699 35.409 51.820 90.00 122.60 90.00 C 1 2 1 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 0.012707 0.000000 0.008126 0.00000 SCALE2 0.000000 0.028241 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022906 0.00000 CONECT 150 898 CONECT 898 150 932 CONECT 932 898 MASTER 271 0 1 2 8 0 0 6 967 2 3 10 END