HEADER CELL ADHESION 31-JUL-09 2WOY TITLE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF STREPTOCOCCUS GORDONII TITLE 2 SURFACE PROTEIN SSPB COMPND MOL_ID: 1; COMPND 2 MOLECULE: AGGLUTININ RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, RESIDUES 1083-1413; COMPND 5 SYNONYM: SSPB-5; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS GORDONII; SOURCE 3 ORGANISM_TAXID: 1302; SOURCE 4 STRAIN: M5; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET-VECTOR KEYWDS CELL ADHESION, CELL WALL, ANTIGEN I/II, PEPTIDOGLYCAN-ANCHOR EXPDTA X-RAY DIFFRACTION AUTHOR N.FORSGREN,K.PERSSON REVDAT 5 16-OCT-24 2WOY 1 REMARK REVDAT 4 05-JUN-24 2WOY 1 REMARK LINK REVDAT 3 13-JUL-11 2WOY 1 VERSN REVDAT 2 23-MAR-10 2WOY 1 JRNL REVDAT 1 16-FEB-10 2WOY 0 JRNL AUTH N.FORSGREN,R.J.LAMONT,K.PERSSON JRNL TITL TWO INTRAMOLECULAR ISOPEPTIDE BONDS ARE IDENTIFIED IN THE JRNL TITL 2 CRYSTAL STRUCTURE OF THE STREPTOCOCCUS GORDONII SSPB JRNL TITL 3 C-TERMINAL DOMAIN. JRNL REF J.MOL.BIOL. V. 397 740 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20138058 JRNL DOI 10.1016/J.JMB.2010.01.065 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 53801 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2740 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 46.8107 - 4.0708 0.99 2760 153 0.1602 0.1703 REMARK 3 2 4.0708 - 3.2314 1.00 2717 131 0.1639 0.1827 REMARK 3 3 3.2314 - 2.8230 1.00 2675 163 0.1792 0.2105 REMARK 3 4 2.8230 - 2.5649 1.00 2670 155 0.1796 0.1894 REMARK 3 5 2.5649 - 2.3810 1.00 2667 140 0.1812 0.2265 REMARK 3 6 2.3810 - 2.2407 1.00 2674 137 0.1824 0.1897 REMARK 3 7 2.2407 - 2.1285 1.00 2687 143 0.1614 0.1779 REMARK 3 8 2.1285 - 2.0358 0.99 2636 158 0.1661 0.2106 REMARK 3 9 2.0358 - 1.9574 0.99 2639 142 0.1677 0.1984 REMARK 3 10 1.9574 - 1.8899 0.99 2577 150 0.1669 0.1915 REMARK 3 11 1.8899 - 1.8308 0.98 2670 136 0.1726 0.2236 REMARK 3 12 1.8308 - 1.7785 0.97 2595 121 0.1656 0.2010 REMARK 3 13 1.7785 - 1.7316 0.96 2545 146 0.1668 0.2177 REMARK 3 14 1.7316 - 1.6894 0.95 2566 135 0.1700 0.2143 REMARK 3 15 1.6894 - 1.6510 0.96 2497 128 0.1767 0.2272 REMARK 3 16 1.6510 - 1.6158 0.94 2532 133 0.1810 0.2560 REMARK 3 17 1.6158 - 1.5835 0.92 2405 145 0.1868 0.2194 REMARK 3 18 1.5835 - 1.5536 0.91 2448 130 0.1842 0.2341 REMARK 3 19 1.5536 - 1.5259 0.82 2134 105 0.2003 0.2363 REMARK 3 20 1.5259 - 1.5000 0.73 1967 89 0.2331 0.2726 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 : 0.38 REMARK 3 B_SOL : 38.73 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.750 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.98970 REMARK 3 B22 (A**2) : -1.26650 REMARK 3 B33 (A**2) : 0.32780 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.35760 REMARK 3 B23 (A**2) : 0.00000 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 : 0.011 2683 REMARK 3 ANGLE : 1.332 3647 REMARK 3 CHIRALITY : 0.096 416 REMARK 3 PLANARITY : 0.006 476 REMARK 3 DIHEDRAL : 16.303 972 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: RESID 1081:1253 REMARK 3 ORIGIN FOR THE GROUP (A): -4.5783 21.3466 40.9020 REMARK 3 T TENSOR REMARK 3 T11: 0.1197 T22: 0.1227 REMARK 3 T33: 0.0742 T12: -0.0272 REMARK 3 T13: -0.0242 T23: 0.0093 REMARK 3 L TENSOR REMARK 3 L11: 0.2121 L22: 0.9830 REMARK 3 L33: 0.2043 L12: -0.0217 REMARK 3 L13: 0.0245 L23: -0.2999 REMARK 3 S TENSOR REMARK 3 S11: 0.0545 S12: -0.0625 S13: -0.0092 REMARK 3 S21: 0.2280 S22: -0.0358 S23: -0.0786 REMARK 3 S31: -0.0640 S32: 0.0108 S33: -0.0002 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: RESID 1254:1413 REMARK 3 ORIGIN FOR THE GROUP (A): -28.4483 19.2307 6.3008 REMARK 3 T TENSOR REMARK 3 T11: 0.0475 T22: 0.0439 REMARK 3 T33: 0.0565 T12: 0.0062 REMARK 3 T13: 0.0069 T23: 0.0008 REMARK 3 L TENSOR REMARK 3 L11: 0.1943 L22: 0.2211 REMARK 3 L33: 0.3320 L12: 0.0395 REMARK 3 L13: 0.0467 L23: -0.1964 REMARK 3 S TENSOR REMARK 3 S11: -0.0006 S12: 0.0066 S13: 0.0018 REMARK 3 S21: 0.0160 S22: 0.0057 S23: -0.0190 REMARK 3 S31: 0.0019 S32: 0.0260 S33: -0.0071 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 2WOY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1290040611. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9754 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55706 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTO-RICKSHAW REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CACL2, 0.1 M HEPES PH 7.5, 20 % REMARK 280 (W/V) PEG 3350 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 25.14500 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 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 HIS A 1058 REMARK 465 HIS A 1059 REMARK 465 HIS A 1060 REMARK 465 HIS A 1061 REMARK 465 HIS A 1062 REMARK 465 HIS A 1063 REMARK 465 PRO A 1064 REMARK 465 MSE A 1065 REMARK 465 SER A 1066 REMARK 465 ASN A 1067 REMARK 465 THR A 1068 REMARK 465 ASN A 1069 REMARK 465 ILE A 1070 REMARK 465 PRO A 1071 REMARK 465 THR A 1072 REMARK 465 THR A 1073 REMARK 465 GLU A 1074 REMARK 465 ASN A 1075 REMARK 465 LEU A 1076 REMARK 465 TYR A 1077 REMARK 465 PRO A 1078 REMARK 465 GLU A 1079 REMARK 465 GLY A 1080 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MSE A1217 C MSE A1217 O 0.237 REMARK 500 MSE A1217 C THR A1218 N 0.232 REMARK 500 MSE A1330 C MSE A1330 O 0.298 REMARK 500 MSE A1330 C LYS A1331 N 0.244 REMARK 500 MSE A1383 C MSE A1383 O 0.160 REMARK 500 MSE A1383 C ARG A1384 N 0.257 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 MSE A1217 O - C - N ANGL. DEV. = -13.8 DEGREES 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 GLN A1275 -164.36 -113.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 MSE A1217 -22.20 REMARK 500 MSE A1383 -14.15 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 A2074 DISTANCE = 6.82 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 CA A2414 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A1133 OD1 REMARK 620 2 TYR A1134 O 92.8 REMARK 620 3 GLU A1136 OE1 171.7 79.1 REMARK 620 4 LYS A1186 O 87.7 168.9 99.9 REMARK 620 5 ALA A1188 O 85.2 95.4 97.2 95.7 REMARK 620 6 HOH A2106 O 88.7 83.2 88.6 85.7 173.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A2415 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A1308 OD1 REMARK 620 2 TYR A1309 O 99.7 REMARK 620 3 GLN A1311 OE1 176.3 79.2 REMARK 620 4 ASN A1354 O 102.3 141.8 80.6 REMARK 620 5 GLY A1355 O 81.4 77.7 101.7 75.1 REMARK 620 6 HOH A2251 O 87.3 74.4 89.0 137.2 147.6 REMARK 620 7 HOH A2315 O 92.7 139.4 86.0 70.2 142.7 67.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A2417 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2052 O REMARK 620 2 HOH A2227 O 98.6 REMARK 620 3 HOH A2272 O 94.5 165.3 REMARK 620 4 HOH A2338 O 74.9 99.8 89.8 REMARK 620 5 HOH A2340 O 150.2 87.7 84.1 75.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 2414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 2415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 2416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 2417 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WD6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE VARIABLE DOMAIN OF THE STREPTOCOCCUS REMARK 900 GORDONII SURFACE PROTEIN SSPB REMARK 900 RELATED ID: 2WZA RELATED DB: PDB REMARK 900 TWO INTRAMOLECULAR ISOPEPTIDE BONDS ARE IDENTIFIED IN THE CRYSTAL REMARK 900 STRUCTURE OF THE STREPTOCOCCUS GORDONII SSPB C-TERMINAL DOMAIN REMARK 900 RELATED ID: 2WQS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF STREPTOCOCCUS REMARK 900 GORDONII SURFACE PROTEIN SSPB DBREF 2WOY A 1083 1413 UNP P16952 SSP5_STRGN 1083 1413 SEQADV 2WOY HIS A 1058 UNP P16952 EXPRESSION TAG SEQADV 2WOY HIS A 1059 UNP P16952 EXPRESSION TAG SEQADV 2WOY HIS A 1060 UNP P16952 EXPRESSION TAG SEQADV 2WOY HIS A 1061 UNP P16952 EXPRESSION TAG SEQADV 2WOY HIS A 1062 UNP P16952 EXPRESSION TAG SEQADV 2WOY HIS A 1063 UNP P16952 EXPRESSION TAG SEQADV 2WOY PRO A 1064 UNP P16952 EXPRESSION TAG SEQADV 2WOY MSE A 1065 UNP P16952 EXPRESSION TAG SEQADV 2WOY SER A 1066 UNP P16952 EXPRESSION TAG SEQADV 2WOY ASN A 1067 UNP P16952 EXPRESSION TAG SEQADV 2WOY THR A 1068 UNP P16952 EXPRESSION TAG SEQADV 2WOY ASN A 1069 UNP P16952 EXPRESSION TAG SEQADV 2WOY ILE A 1070 UNP P16952 EXPRESSION TAG SEQADV 2WOY PRO A 1071 UNP P16952 EXPRESSION TAG SEQADV 2WOY THR A 1072 UNP P16952 EXPRESSION TAG SEQADV 2WOY THR A 1073 UNP P16952 EXPRESSION TAG SEQADV 2WOY GLU A 1074 UNP P16952 EXPRESSION TAG SEQADV 2WOY ASN A 1075 UNP P16952 EXPRESSION TAG SEQADV 2WOY LEU A 1076 UNP P16952 EXPRESSION TAG SEQADV 2WOY TYR A 1077 UNP P16952 EXPRESSION TAG SEQADV 2WOY PRO A 1078 UNP P16952 EXPRESSION TAG SEQADV 2WOY GLU A 1079 UNP P16952 EXPRESSION TAG SEQADV 2WOY GLY A 1080 UNP P16952 EXPRESSION TAG SEQADV 2WOY ALA A 1081 UNP P16952 EXPRESSION TAG SEQADV 2WOY MSE A 1082 UNP P16952 EXPRESSION TAG SEQRES 1 A 356 HIS HIS HIS HIS HIS HIS PRO MSE SER ASN THR ASN ILE SEQRES 2 A 356 PRO THR THR GLU ASN LEU TYR PRO GLU GLY ALA MSE VAL SEQRES 3 A 356 ASN LYS ASN LYS GLU GLY LEU ASN ILE ASP GLY LYS GLU SEQRES 4 A 356 VAL LEU ALA GLY SER THR ASN TYR TYR GLU LEU THR TRP SEQRES 5 A 356 ASP LEU ASP GLN TYR LYS GLY ASP LYS SER SER LYS GLU SEQRES 6 A 356 ALA ILE GLN ASN GLY PHE TYR TYR VAL ASP ASP TYR PRO SEQRES 7 A 356 GLU GLU ALA LEU ASP VAL ARG PRO ASP LEU VAL LYS VAL SEQRES 8 A 356 ALA ASP GLU LYS GLY ASN GLN VAL SER GLY VAL SER VAL SEQRES 9 A 356 GLN GLN TYR ASP SER LEU GLU ALA ALA PRO LYS LYS VAL SEQRES 10 A 356 GLN ASP LEU LEU LYS LYS ALA ASN ILE THR VAL LYS GLY SEQRES 11 A 356 ALA PHE GLN LEU PHE SER ALA ASP ASN PRO GLU GLU PHE SEQRES 12 A 356 TYR LYS GLN TYR VAL ALA THR GLY THR SER LEU VAL ILE SEQRES 13 A 356 THR ASP PRO MSE THR VAL LYS SER GLU PHE GLY LYS THR SEQRES 14 A 356 GLY GLY LYS TYR GLU ASN LYS ALA TYR GLN ILE ASP PHE SEQRES 15 A 356 GLY ASN GLY TYR ALA THR GLU VAL VAL VAL ASN ASN VAL SEQRES 16 A 356 PRO LYS ILE THR PRO LYS LYS ASP VAL THR VAL SER LEU SEQRES 17 A 356 ASP PRO THR SER GLU ASN LEU ASP GLY GLN THR VAL GLN SEQRES 18 A 356 LEU TYR GLN THR PHE ASN TYR ARG LEU ILE GLY GLY LEU SEQRES 19 A 356 ILE PRO GLN ASN HIS SER GLU GLU LEU GLU ASP TYR SER SEQRES 20 A 356 PHE VAL ASP ASP TYR ASP GLN ALA GLY ASP GLN TYR THR SEQRES 21 A 356 GLY ASN TYR LYS THR PHE SER SER LEU ASN LEU THR MSE SEQRES 22 A 356 LYS ASP GLY SER VAL ILE LYS ALA GLY THR ASP LEU THR SEQRES 23 A 356 SER GLN THR THR ALA GLU THR ASP ALA THR ASN GLY ILE SEQRES 24 A 356 VAL THR VAL ARG PHE LYS GLU ASP PHE LEU GLN LYS ILE SEQRES 25 A 356 SER LEU ASP SER PRO PHE GLN ALA GLU THR TYR LEU GLN SEQRES 26 A 356 MSE ARG ARG ILE ALA ILE GLY THR PHE GLU ASN THR TYR SEQRES 27 A 356 VAL ASN THR VAL ASN LYS VAL ALA TYR ALA SER ASN THR SEQRES 28 A 356 VAL ARG THR THR THR MODRES 2WOY MSE A 1082 MET SELENOMETHIONINE MODRES 2WOY MSE A 1217 MET SELENOMETHIONINE MODRES 2WOY MSE A 1330 MET SELENOMETHIONINE MODRES 2WOY MSE A 1383 MET SELENOMETHIONINE HET MSE A1082 8 HET MSE A1217 8 HET MSE A1330 8 HET MSE A1383 8 HET CA A2414 1 HET CA A2415 1 HET CA A2416 1 HET CA A2417 1 HETNAM MSE SELENOMETHIONINE HETNAM CA CALCIUM ION FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 CA 4(CA 2+) FORMUL 6 HOH *372(H2 O) HELIX 1 1 LEU A 1111 LYS A 1115 5 5 HELIX 2 2 SER A 1120 GLN A 1125 1 6 HELIX 3 3 PRO A 1143 VAL A 1146 5 4 HELIX 4 4 PRO A 1171 ASN A 1182 1 12 HELIX 5 5 ASN A 1196 TYR A 1204 1 9 HELIX 6 6 SER A 1221 THR A 1226 5 6 HELIX 7 7 LEU A 1342 SER A 1344 5 3 HELIX 8 8 LYS A 1362 GLN A 1367 1 6 SHEET 1 AA 4 MSE A1082 VAL A1083 0 SHEET 2 AA 4 THR A1102 TRP A1109 -1 O GLU A1106 N VAL A1083 SHEET 3 AA 4 LEU A1211 VAL A1219 -1 O LEU A1211 N TRP A1109 SHEET 4 AA 4 LYS A1147 ALA A1149 1 O LYS A1147 N THR A1214 SHEET 1 AB 4 MSE A1082 VAL A1083 0 SHEET 2 AB 4 THR A1102 TRP A1109 -1 O GLU A1106 N VAL A1083 SHEET 3 AB 4 LEU A1211 VAL A1219 -1 O LEU A1211 N TRP A1109 SHEET 4 AB 4 LEU A1139 VAL A1141 -1 O ASP A1140 N THR A1218 SHEET 1 AC 2 LYS A1147 ALA A1149 0 SHEET 2 AC 2 LEU A1211 VAL A1219 1 O VAL A1212 N ALA A1149 SHEET 1 AD 5 VAL A1159 TYR A1164 0 SHEET 2 AD 5 PHE A1189 ALA A1194 -1 O PHE A1189 N TYR A1164 SHEET 3 AD 5 PHE A1128 ASP A1133 -1 O PHE A1128 N ALA A1194 SHEET 4 AD 5 GLY A1228 ASP A1238 -1 O LYS A1233 N ASP A1133 SHEET 5 AD 5 ASN A1241 VAL A1252 -1 O ASN A1241 N ASP A1238 SHEET 1 AE 4 LYS A1258 THR A1262 0 SHEET 2 AE 4 THR A1282 ILE A1288 -1 O ASN A1284 N THR A1262 SHEET 3 AE 4 ALA A1377 ARG A1385 -1 O THR A1379 N LEU A1287 SHEET 4 AE 4 ASP A1314 SER A1324 -1 O GLN A1315 N ARG A1384 SHEET 1 AF 5 THR A1346 ASP A1351 0 SHEET 2 AF 5 ILE A1356 PHE A1361 -1 O ILE A1356 N ASP A1351 SHEET 3 AF 5 TYR A1303 ASP A1308 -1 O TYR A1303 N PHE A1361 SHEET 4 AF 5 VAL A1396 VAL A1399 -1 O VAL A1396 N VAL A1306 SHEET 5 AF 5 VAL A1402 ALA A1405 -1 O VAL A1402 N VAL A1399 SHEET 1 AG 2 LEU A1328 THR A1329 0 SHEET 2 AG 2 VAL A1335 ILE A1336 -1 O ILE A1336 N LEU A1328 SHEET 1 AH 2 GLY A1389 ASN A1393 0 SHEET 2 AH 2 VAL A1409 THR A1413 -1 O VAL A1409 N ASN A1393 LINK C ALA A1081 N MSE A1082 1555 1555 1.33 LINK C MSE A1082 N VAL A1083 1555 1555 1.33 LINK C PRO A1216 N MSE A1217 1555 1555 1.33 LINK C MSE A1217 N THR A1218 1555 1555 1.57 LINK NZ LYS A1259 CG ASN A1393 1555 1555 1.43 LINK C THR A1329 N MSE A1330 1555 1555 1.32 LINK C MSE A1330 N LYS A1331 1555 1555 1.58 LINK C GLN A1382 N MSE A1383 1555 1555 1.33 LINK C MSE A1383 N ARG A1384 1555 1555 1.59 LINK OD1 ASP A1133 CA CA A2414 1555 1555 2.36 LINK O TYR A1134 CA CA A2414 1555 1555 2.38 LINK OE1 GLU A1136 CA CA A2414 1555 1555 2.41 LINK O GLN A1163 CA CA A2416 1555 1555 2.36 LINK O LYS A1186 CA CA A2414 1555 1555 2.31 LINK O ALA A1188 CA CA A2414 1555 1555 2.41 LINK OD1 ASP A1308 CA CA A2415 1555 1555 2.24 LINK O TYR A1309 CA CA A2415 1555 1555 2.38 LINK OE1 GLN A1311 CA CA A2415 1555 1555 2.38 LINK O ASN A1354 CA CA A2415 1555 1555 2.43 LINK O GLY A1355 CA CA A2415 1555 1555 2.62 LINK O HOH A2052 CA CA A2417 1555 1555 2.49 LINK O HOH A2106 CA CA A2414 1555 1555 2.43 LINK O HOH A2227 CA CA A2417 1555 1555 2.47 LINK O HOH A2251 CA CA A2415 1555 1555 2.49 LINK O HOH A2272 CA CA A2417 1555 1555 2.42 LINK O HOH A2315 CA CA A2415 1555 1555 2.54 LINK O HOH A2338 CA CA A2417 1555 1555 2.43 LINK O HOH A2340 CA CA A2417 1555 1555 2.54 SITE 1 AC1 6 ASP A1133 TYR A1134 GLU A1136 LYS A1186 SITE 2 AC1 6 ALA A1188 HOH A2106 SITE 1 AC2 7 ASP A1308 TYR A1309 GLN A1311 ASN A1354 SITE 2 AC2 7 GLY A1355 HOH A2251 HOH A2315 SITE 1 AC3 1 GLN A1163 SITE 1 AC4 5 HOH A2052 HOH A2227 HOH A2272 HOH A2338 SITE 2 AC4 5 HOH A2340 CRYST1 37.745 50.290 94.370 90.00 97.44 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 0.026494 0.000000 0.003460 0.00000 SCALE2 0.000000 0.019885 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010687 0.00000