HEADER PROTEIN BINDING 21-NOV-13 4NPD TITLE HIGH-RESOLUTION STRUCTURE OF C DOMAIN OF STAPHYLOCOCCAL PROTEIN A AT TITLE 2 CRYOGENIC TEMPERATURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMMUNOGLOBULIN G-BINDING PROTEIN A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 270-327; COMPND 5 SYNONYM: IGG-BINDING PROTEIN A, STAPHYLOCOCCAL PROTEIN A; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: C DOMAIN OF STAPHYLOCOCCAL PROTEIN A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 STRAIN: 8325-4; SOURCE 5 GENE: PROTEIN A, SPA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PAED4 KEYWDS SPA, THREE-HELIX BUNDLE, CONFORMATIONAL HETEROGENEITY, RAPIDLY KEYWDS 2 UNFOLDING AND FOLDING, RUF, ANTIBODY BINDING, ANTIBODY, TNFR1, VON KEYWDS 3 WILLEBRAND FACTOR, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR L.N.DEIS,C.W.PEMBLE IV,T.G.OAS,J.S.RICHARDSON,D.C.RICHARDSON REVDAT 4 28-FEB-24 4NPD 1 REMARK LINK REVDAT 3 22-NOV-17 4NPD 1 REMARK REVDAT 2 22-OCT-14 4NPD 1 JRNL REVDAT 1 08-OCT-14 4NPD 0 JRNL AUTH L.N.DEIS,C.W.PEMBLE,Y.QI,A.HAGARMAN,D.C.RICHARDSON, JRNL AUTH 2 J.S.RICHARDSON,T.G.OAS JRNL TITL MULTISCALE CONFORMATIONAL HETEROGENEITY IN STAPHYLOCOCCAL JRNL TITL 2 PROTEIN A: POSSIBLE DETERMINANT OF FUNCTIONAL PLASTICITY. JRNL REF STRUCTURE V. 22 1467 2014 JRNL REFN ISSN 0969-2126 JRNL PMID 25295398 JRNL DOI 10.1016/J.STR.2014.08.014 REMARK 2 REMARK 2 RESOLUTION. 0.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1664 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) : 0.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 37063 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.113 REMARK 3 R VALUE (WORKING SET) : 0.112 REMARK 3 FREE R VALUE : 0.130 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.220 REMARK 3 FREE R VALUE TEST SET COUNT : 1934 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 25.4013 - 2.1683 1.00 2693 152 0.1470 0.1604 REMARK 3 2 2.1683 - 1.7211 1.00 2641 144 0.1221 0.1363 REMARK 3 3 1.7211 - 1.5036 1.00 2646 137 0.0994 0.1268 REMARK 3 4 1.5036 - 1.3661 1.00 2608 152 0.0918 0.1123 REMARK 3 5 1.3661 - 1.2682 0.99 2614 152 0.0882 0.1180 REMARK 3 6 1.2682 - 1.1935 0.99 2593 136 0.0836 0.1098 REMARK 3 7 1.1935 - 1.1337 0.99 2596 133 0.0787 0.0846 REMARK 3 8 1.1337 - 1.0843 0.98 2590 143 0.0797 0.0906 REMARK 3 9 1.0843 - 1.0426 0.97 2522 145 0.0864 0.1042 REMARK 3 10 1.0426 - 1.0066 0.97 2548 145 0.0959 0.1145 REMARK 3 11 1.0066 - 0.9751 0.96 2540 115 0.1000 0.1287 REMARK 3 12 0.9751 - 0.9473 0.94 2478 150 0.1144 0.1399 REMARK 3 13 0.9473 - 0.9223 0.85 2215 121 0.1259 0.1433 REMARK 3 14 0.9223 - 0.9000 0.70 1845 109 0.1438 0.1524 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) : 0.040 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 10.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.38 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 : 0.013 867 REMARK 3 ANGLE : 1.552 1178 REMARK 3 CHIRALITY : 0.087 126 REMARK 3 PLANARITY : 0.010 163 REMARK 3 DIHEDRAL : 15.719 355 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 4NPD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000083488. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID 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 : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37877 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.19700 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: SAD REMARK 200 SOFTWARE USED: SHELX, SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA THIOCYANATE, PEG 3350, GLYCEROL, PH REMARK 280 7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 19.20500 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 297 O HOH A 306 2.11 REMARK 500 O HOH A 281 O HOH A 299 2.13 REMARK 500 O HOH A 295 O HOH A 301 2.14 REMARK 500 O HOH A 318 O HOH A 319 2.15 REMARK 500 O HOH A 311 O HOH A 321 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 HE2 HIS A 18 ZN ZN A 101 2747 1.11 REMARK 500 O HOH A 301 O HOH A 325 2545 1.97 REMARK 500 O HOH A 299 O HOH A 302 2656 1.98 REMARK 500 NZ LYS A 58 O HOH A 253 2656 2.12 REMARK 500 O HOH A 319 O HOH A 333 2746 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 37 97.83 -162.99 REMARK 500 REMARK 500 REMARK: NULL 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 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A 20 O REMARK 620 2 PRO A 20 O 2.4 REMARK 620 3 HOH A 221 O 84.3 83.6 REMARK 620 4 HOH A 264 O 87.9 90.1 85.2 REMARK 620 5 HOH A 330 O 96.9 94.5 90.5 173.3 REMARK 620 6 HOH A 332 O 135.3 133.0 71.3 125.1 48.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 58 OXT REMARK 620 2 LYS A 58 OXT 1.1 REMARK 620 3 SCN A 103 N 119.2 119.4 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCN A 103 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NPE RELATED DB: PDB REMARK 900 RELATED ID: 4NPF RELATED DB: PDB DBREF 4NPD A 1 58 UNP P38507 SPA_STAAU 270 327 SEQRES 1 A 58 ALA ASP ASN LYS PHE ASN LYS GLU GLN GLN ASN ALA PHE SEQRES 2 A 58 TYR GLU ILE LEU HIS LEU PRO ASN LEU THR GLU GLU GLN SEQRES 3 A 58 ARG ASN GLY PHE ILE GLN SER LEU LYS ASP ASP PRO SER SEQRES 4 A 58 VAL SER LYS GLU ILE LEU ALA GLU ALA LYS LYS LEU ASN SEQRES 5 A 58 ASP ALA GLN ALA PRO LYS HET ZN A 101 1 HET ZN A 102 1 HET SCN A 103 3 HETNAM ZN ZINC ION HETNAM SCN THIOCYANATE ION FORMUL 2 ZN 2(ZN 2+) FORMUL 4 SCN C N S 1- FORMUL 5 HOH *134(H2 O) HELIX 1 1 ASN A 6 LEU A 19 1 14 HELIX 2 2 THR A 23 ASP A 37 1 15 HELIX 3 3 VAL A 40 GLN A 55 1 16 LINK O APRO A 20 ZN ZN A 102 1555 1555 1.91 LINK O BPRO A 20 ZN ZN A 102 1555 1555 2.09 LINK OXTBLYS A 58 ZN ZN A 101 1555 1555 1.94 LINK OXTALYS A 58 ZN ZN A 101 1555 1555 2.03 LINK ZN ZN A 101 N SCN A 103 1555 1555 1.91 LINK ZN ZN A 102 O HOH A 221 1555 1555 2.15 LINK ZN ZN A 102 O HOH A 264 1555 1555 2.33 LINK ZN ZN A 102 O AHOH A 330 1555 1555 1.98 LINK ZN ZN A 102 O HOH A 332 1555 1555 2.65 SITE 1 AC1 3 GLU A 47 LYS A 58 SCN A 103 SITE 1 AC2 6 PRO A 20 HOH A 221 HOH A 228 HOH A 264 SITE 2 AC2 6 HOH A 330 HOH A 332 SITE 1 AC3 6 GLY A 29 PHE A 30 SER A 33 GLU A 47 SITE 2 AC3 6 LYS A 58 ZN A 101 CRYST1 27.250 38.410 28.610 90.00 117.44 90.00 P 1 21 1 2 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 0.036697 0.000000 0.019055 0.00000 SCALE2 0.000000 0.026035 0.000000 0.00000 SCALE3 0.000000 0.000000 0.039384 0.00000