HEADER SIGNALING PROTEIN 19-SEP-14 4WH4 TITLE PROTEIN GB1 QUADRUPLE MUTANT I6H/N8H/K28H/Q32H 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; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS SP. GROUP G; SOURCE 3 ORGANISM_TAXID: 1320; SOURCE 4 GENE: SPG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IMMUNOGLOBULIN-BINDING DOMAIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.C.CUNNINGHAM,W.S.HORNE,S.SAXENA REVDAT 3 27-NOV-19 4WH4 1 REMARK REVDAT 2 06-SEP-17 4WH4 1 JRNL REMARK REVDAT 1 05-AUG-15 4WH4 0 JRNL AUTH T.F.CUNNINGHAM,M.R.PUTTERMAN,A.DESAI,W.S.HORNE,S.SAXENA JRNL TITL THE DOUBLE-HISTIDINE CU2+-BINDING MOTIF: A HIGHLY RIGID, JRNL TITL 2 SITE-SPECIFIC SPIN PROBE FOR ELECTRON SPIN RESONANCE JRNL TITL 3 DISTANCE MEASUREMENTS. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 54 6330 2015 JRNL REFN ESSN 1521-3773 JRNL PMID 25821033 JRNL DOI 10.1002/ANIE.201501968 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1690) 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 6837 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.190 REMARK 3 FREE R VALUE TEST SET COUNT : 697 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 32.1709 - 3.7604 1.00 1281 151 0.1687 0.2039 REMARK 3 2 3.7604 - 2.9854 1.00 1245 137 0.1973 0.2834 REMARK 3 3 2.9854 - 2.6082 0.99 1223 135 0.2535 0.3180 REMARK 3 4 2.6082 - 2.3698 0.99 1191 139 0.2536 0.2923 REMARK 3 5 2.3698 - 2.2000 0.98 1200 135 0.2647 0.3351 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.210 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 : 0.004 937 REMARK 3 ANGLE : 0.647 1265 REMARK 3 CHIRALITY : 0.023 138 REMARK 3 PLANARITY : 0.002 158 REMARK 3 DIHEDRAL : 13.947 318 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 4WH4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000203802. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : RIGAKU VARIMAX OPTICS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6876 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 32.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 2QMT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.75 M AMMONIUM SULFATE, 0.2 M SODIUM REMARK 280 CHLORIDE, 0.1 M HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-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 13.77333 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 27.54667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.54667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 13.77333 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 102 DBREF 4WH4 A 3 56 UNP P19909 SPG2_STRSG 304 357 DBREF 4WH4 B 3 56 UNP P19909 SPG2_STRSG 304 357 SEQADV 4WH4 MET A 1 UNP P19909 EXPRESSION TAG SEQADV 4WH4 GLN A 2 UNP P19909 EXPRESSION TAG SEQADV 4WH4 HIS A 6 UNP P19909 ILE 307 ENGINEERED MUTATION SEQADV 4WH4 HIS A 8 UNP P19909 ASN 309 ENGINEERED MUTATION SEQADV 4WH4 HIS A 28 UNP P19909 LYS 329 ENGINEERED MUTATION SEQADV 4WH4 HIS A 32 UNP P19909 GLN 333 ENGINEERED MUTATION SEQADV 4WH4 MET B 1 UNP P19909 EXPRESSION TAG SEQADV 4WH4 GLN B 2 UNP P19909 EXPRESSION TAG SEQADV 4WH4 HIS B 6 UNP P19909 ILE 307 ENGINEERED MUTATION SEQADV 4WH4 HIS B 8 UNP P19909 ASN 309 ENGINEERED MUTATION SEQADV 4WH4 HIS B 28 UNP P19909 LYS 329 ENGINEERED MUTATION SEQADV 4WH4 HIS B 32 UNP P19909 GLN 333 ENGINEERED MUTATION SEQRES 1 A 56 MET GLN TYR LYS LEU HIS LEU HIS 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 HIS VAL PHE LYS HIS TYR ALA ASN ASP ASN 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 HIS LEU HIS 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 HIS VAL PHE LYS HIS TYR ALA ASN ASP ASN 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 SO4 A 101 5 HET GOL A 102 6 HET GOL A 103 6 HET GOL A 104 6 HET GOL B 101 6 HET GOL B 102 6 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 SO4 O4 S 2- FORMUL 4 GOL 5(C3 H8 O3) FORMUL 9 HOH *29(H2 O) HELIX 1 AA1 ASP A 22 ASN A 37 1 16 HELIX 2 AA2 ASP A 47 THR A 49 5 3 HELIX 3 AA3 ASP B 22 ASN B 37 1 16 SHEET 1 AA1 4 LYS A 13 GLU A 19 0 SHEET 2 AA1 4 GLN A 2 HIS A 8 -1 N LEU A 5 O THR A 16 SHEET 3 AA1 4 THR A 51 THR A 55 1 O PHE A 52 N HIS A 6 SHEET 4 AA1 4 GLU A 42 ASP A 46 -1 N THR A 44 O THR A 53 SHEET 1 AA2 4 LYS B 13 GLU B 19 0 SHEET 2 AA2 4 GLN B 2 HIS B 8 -1 N LEU B 5 O THR B 16 SHEET 3 AA2 4 THR B 51 THR B 55 1 O PHE B 52 N LYS B 4 SHEET 4 AA2 4 GLU B 42 ASP B 46 -1 N GLU B 42 O THR B 55 SITE 1 AC1 5 THR A 17 THR A 18 GLU A 19 GOL A 103 SITE 2 AC1 5 HIS B 28 SITE 1 AC2 5 TYR A 33 ASP A 36 GOL A 103 HIS B 28 SITE 2 AC2 5 HOH B 201 SITE 1 AC3 6 THR A 17 PHE A 30 TYR A 33 SO4 A 101 SITE 2 AC3 6 GOL A 102 HIS B 28 SITE 1 AC4 5 ALA A 24 GLU A 27 TYR A 45 PHE A 52 SITE 2 AC4 5 GLU B 56 SITE 1 AC5 4 ALA A 48 LYS A 50 GLU B 27 TRP B 43 SITE 1 AC6 6 MET B 1 TYR B 3 ASP B 22 ALA B 23 SITE 2 AC6 6 ASP B 47 LYS B 50 CRYST1 74.287 74.287 41.320 90.00 90.00 120.00 P 31 2 1 12 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 0.013461 0.007772 0.000000 0.00000 SCALE2 0.000000 0.015544 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024201 0.00000 MASTER 232 0 6 3 8 0 11 6 0 0 0 10 END