HEADER BIOSYNTHETIC PROTEIN 22-JAN-19 6NR6 TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCUS PSEUDINTERMEDIUS SBNI IN COMPLEX TITLE 2 WITH ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL TRANSCRIPTIONAL REGULATOR/O-PHOSPHO-L-SERINE COMPND 3 SYNTHASE SBNI; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS PSEUDINTERMEDIUS; SOURCE 3 ORGANISM_TAXID: 283734; SOURCE 4 GENE: SBNI, DD902_02060, DD924_03760, DV946_04660, DV961_07520; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS FREE SERINE KINASE, SIDEROPHORE, PARB/SRX FAMILY, STAPHYLOFERRIN B, KEYWDS 2 BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.M.VERSTRAETE,L.D.MORALES,M.J.KOBYLARZ,S.A.LOUTET,H.A.LAAKSO, AUTHOR 2 D.E.HEINRICHS,M.E.P.MURPHY REVDAT 4 11-OCT-23 6NR6 1 REMARK REVDAT 3 30-DEC-20 6NR6 1 JRNL LINK REVDAT 2 08-JAN-20 6NR6 1 REMARK REVDAT 1 19-JUN-19 6NR6 0 JRNL AUTH M.M.VERSTRAETE,L.D.MORALES,M.J.KOBYLARZ,S.A.LOUTET, JRNL AUTH 2 H.A.LAAKSO,T.B.PINTER,M.J.STILLMAN,D.E.HEINRICHS, JRNL AUTH 3 M.E.P.MURPHY JRNL TITL THE HEME-SENSITIVE REGULATOR SBNI HAS A BIFUNCTIONAL ROLE IN JRNL TITL 2 STAPHYLOFERRIN B PRODUCTION BY STAPHYLOCOCCUS AUREUS . JRNL REF J.BIOL.CHEM. V. 294 11622 2019 JRNL REFN ESSN 1083-351X JRNL PMID 31197035 JRNL DOI 10.1074/JBC.RA119.007757 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 52321 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.820 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 37.8185 - 4.5763 1.00 3830 153 0.1813 0.2098 REMARK 3 2 4.5763 - 3.6332 1.00 3672 145 0.1741 0.2122 REMARK 3 3 3.6332 - 3.1742 1.00 3649 145 0.2059 0.2126 REMARK 3 4 3.1742 - 2.8841 1.00 3623 144 0.2342 0.2567 REMARK 3 5 2.8841 - 2.6775 1.00 3614 142 0.2359 0.2735 REMARK 3 6 2.6775 - 2.5196 1.00 3578 143 0.2350 0.3008 REMARK 3 7 2.5196 - 2.3935 1.00 3580 142 0.2358 0.3131 REMARK 3 8 2.3935 - 2.2893 1.00 3567 142 0.2314 0.2921 REMARK 3 9 2.2893 - 2.2012 1.00 3573 142 0.2228 0.2896 REMARK 3 10 2.2012 - 2.1252 1.00 3556 142 0.2317 0.2837 REMARK 3 11 2.1252 - 2.0588 1.00 3580 142 0.2454 0.2838 REMARK 3 12 2.0588 - 1.9999 1.00 3553 142 0.2565 0.2980 REMARK 3 13 1.9999 - 1.9473 0.99 3527 139 0.2724 0.2974 REMARK 3 14 1.9473 - 1.8998 0.96 3419 137 0.3100 0.3367 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.290 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.51 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 : 0.006 4241 REMARK 3 ANGLE : 0.739 5766 REMARK 3 CHIRALITY : 0.049 652 REMARK 3 PLANARITY : 0.004 724 REMARK 3 DIHEDRAL : 17.468 2572 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 68 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.5139 15.5135 -34.7706 REMARK 3 T TENSOR REMARK 3 T11: 0.2711 T22: 0.2171 REMARK 3 T33: 0.2504 T12: 0.0092 REMARK 3 T13: -0.0321 T23: -0.0272 REMARK 3 L TENSOR REMARK 3 L11: 4.2134 L22: 4.9897 REMARK 3 L33: 3.5477 L12: -0.2134 REMARK 3 L13: -0.3336 L23: -0.3427 REMARK 3 S TENSOR REMARK 3 S11: -0.0863 S12: -0.0672 S13: 0.0787 REMARK 3 S21: 0.1159 S22: 0.0105 S23: 0.0086 REMARK 3 S31: 0.1438 S32: 0.0034 S33: 0.0601 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 69 THROUGH 93 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.2040 13.1059 -43.2385 REMARK 3 T TENSOR REMARK 3 T11: 0.2653 T22: 0.1304 REMARK 3 T33: 0.2827 T12: 0.0420 REMARK 3 T13: 0.0101 T23: 0.0654 REMARK 3 L TENSOR REMARK 3 L11: 5.4080 L22: 2.5457 REMARK 3 L33: 3.1842 L12: 0.9468 REMARK 3 L13: 1.1225 L23: 1.3272 REMARK 3 S TENSOR REMARK 3 S11: 0.0828 S12: 0.4016 S13: -0.0557 REMARK 3 S21: -0.0658 S22: 0.1803 S23: -0.2913 REMARK 3 S31: -0.0397 S32: 0.2494 S33: -0.2270 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 94 THROUGH 150 ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.3179 9.5407 -55.2554 REMARK 3 T TENSOR REMARK 3 T11: 0.4045 T22: 0.3275 REMARK 3 T33: 0.5090 T12: 0.0202 REMARK 3 T13: -0.1703 T23: -0.0073 REMARK 3 L TENSOR REMARK 3 L11: 5.4354 L22: 8.1857 REMARK 3 L33: 2.0884 L12: 1.5571 REMARK 3 L13: -0.3221 L23: -1.6028 REMARK 3 S TENSOR REMARK 3 S11: -0.0792 S12: 0.1552 S13: 0.7646 REMARK 3 S21: -0.6999 S22: 0.0371 S23: 1.0141 REMARK 3 S31: -0.0034 S32: -0.2455 S33: 0.0286 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 151 THROUGH 205 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.6612 8.6209 -50.1339 REMARK 3 T TENSOR REMARK 3 T11: 0.3191 T22: 0.2994 REMARK 3 T33: 0.2121 T12: 0.0098 REMARK 3 T13: -0.0324 T23: 0.0072 REMARK 3 L TENSOR REMARK 3 L11: 5.1337 L22: 8.0705 REMARK 3 L33: 1.7080 L12: 4.7053 REMARK 3 L13: 2.4174 L23: 2.7358 REMARK 3 S TENSOR REMARK 3 S11: 0.0225 S12: 0.1618 S13: -0.0896 REMARK 3 S21: -0.1349 S22: 0.0386 S23: 0.0168 REMARK 3 S31: 0.0550 S32: 0.0666 S33: -0.0811 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 206 THROUGH 225 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.8806 14.9362 -28.3700 REMARK 3 T TENSOR REMARK 3 T11: 0.4509 T22: 0.2809 REMARK 3 T33: 0.3704 T12: 0.0166 REMARK 3 T13: -0.0579 T23: 0.0038 REMARK 3 L TENSOR REMARK 3 L11: 7.5988 L22: 2.1201 REMARK 3 L33: 2.7711 L12: -1.6303 REMARK 3 L13: -2.0664 L23: -1.2625 REMARK 3 S TENSOR REMARK 3 S11: 0.0297 S12: -0.8085 S13: 0.5327 REMARK 3 S21: 0.3476 S22: 0.0658 S23: -0.2585 REMARK 3 S31: -0.5958 S32: 0.2861 S33: -0.0113 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 226 THROUGH 254 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.5747 6.8277 -32.9973 REMARK 3 T TENSOR REMARK 3 T11: 0.3027 T22: 0.3094 REMARK 3 T33: 0.4010 T12: 0.1253 REMARK 3 T13: -0.0912 T23: 0.0773 REMARK 3 L TENSOR REMARK 3 L11: 4.5548 L22: 8.4373 REMARK 3 L33: 7.7483 L12: 5.0888 REMARK 3 L13: 2.7155 L23: 5.8164 REMARK 3 S TENSOR REMARK 3 S11: -0.0360 S12: -0.1128 S13: 0.0891 REMARK 3 S21: 0.0184 S22: 0.1318 S23: -0.2635 REMARK 3 S31: -0.1817 S32: 0.4609 S33: -0.0172 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 80 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.9333 -17.9281 -88.4568 REMARK 3 T TENSOR REMARK 3 T11: 0.4925 T22: 0.5244 REMARK 3 T33: 0.4852 T12: 0.0409 REMARK 3 T13: 0.2121 T23: -0.0975 REMARK 3 L TENSOR REMARK 3 L11: 8.0587 L22: 6.8064 REMARK 3 L33: 7.5069 L12: -1.4909 REMARK 3 L13: -0.7892 L23: -1.1104 REMARK 3 S TENSOR REMARK 3 S11: -0.3756 S12: 0.2163 S13: -1.2052 REMARK 3 S21: 0.0050 S22: -0.2685 S23: 0.4645 REMARK 3 S31: 0.5204 S32: -0.0646 S33: 0.6261 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 81 THROUGH 226 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.2161 -21.5915 -71.6051 REMARK 3 T TENSOR REMARK 3 T11: 0.7055 T22: 0.5228 REMARK 3 T33: 0.5434 T12: 0.1025 REMARK 3 T13: 0.2261 T23: 0.0713 REMARK 3 L TENSOR REMARK 3 L11: 5.5911 L22: 0.1797 REMARK 3 L33: 3.5428 L12: 1.1156 REMARK 3 L13: -3.2939 L23: -1.6404 REMARK 3 S TENSOR REMARK 3 S11: -0.6705 S12: -0.4719 S13: -1.0344 REMARK 3 S21: -0.3049 S22: -0.0824 S23: -0.2043 REMARK 3 S31: 0.6552 S32: 0.1670 S33: 0.6531 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 227 THROUGH 254 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.5618 -2.6789 -90.6615 REMARK 3 T TENSOR REMARK 3 T11: 0.5763 T22: 0.5862 REMARK 3 T33: 0.2902 T12: -0.0702 REMARK 3 T13: -0.0002 T23: 0.2146 REMARK 3 L TENSOR REMARK 3 L11: 8.5042 L22: 5.6004 REMARK 3 L33: 8.0666 L12: -5.7168 REMARK 3 L13: -4.0004 L23: 5.6455 REMARK 3 S TENSOR REMARK 3 S11: -0.1282 S12: 0.7428 S13: 0.8450 REMARK 3 S21: -0.0973 S22: -0.0406 S23: -0.4844 REMARK 3 S31: 0.1125 S32: 0.6127 S33: 0.1120 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 6NR6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1000239216. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97896 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52452 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 37.811 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.86700 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 2.7.16 REMARK 200 STARTING MODEL: 5UJD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.16 M CALCIUM ACETATE, 0.1 M REMARK 280 IMIDAZOLE (PH 8), 8% (V/V) PEG 8000, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 50.82200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.53700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 50.82200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.53700 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 51070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -158.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 GLU B 106 CG CD OE1 OE2 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 OE2 GLU B 105 N LEU B 108 1.98 REMARK 500 OD2 ASP A 58 NH2 ARG A 208 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 LYS A 2 5.22 -69.33 REMARK 500 LEU A 224 -149.14 -103.84 REMARK 500 GLU A 252 72.80 -106.43 REMARK 500 GLU B 105 86.66 -68.23 REMARK 500 ASN B 211 31.45 73.19 REMARK 500 GLN B 213 73.35 54.79 REMARK 500 ASN B 226 -1.58 -155.75 REMARK 500 GLU B 252 68.68 -105.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 ADP A 304 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 MG A 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 58 OD1 REMARK 620 2 ADP A 304 O1A 155.0 REMARK 620 3 ADP A 304 O1B 87.4 73.0 REMARK 620 4 HOH A 514 O 89.3 77.7 96.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A 94 O REMARK 620 2 ASP A 170 OD1 171.2 REMARK 620 3 ASP A 170 OD2 135.7 52.8 REMARK 620 4 ASN A 172 OD1 76.1 111.0 75.0 REMARK 620 5 ASP A 173 OD2 83.1 98.5 78.0 112.5 REMARK 620 6 HOH A 480 O 90.2 86.2 115.6 78.6 165.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 101 O REMARK 620 2 HOH A 401 O 81.6 REMARK 620 3 HOH A 417 O 98.9 133.9 REMARK 620 4 HOH A 439 O 165.0 89.7 78.4 REMARK 620 5 HOH A 531 O 108.9 81.1 138.7 81.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 58 OD1 REMARK 620 2 ADP B 303 O3B 75.8 REMARK 620 3 ADP B 303 O2A 124.4 61.3 REMARK 620 4 HOH B 414 O 65.6 103.6 90.9 REMARK 620 5 HOH B 427 O 116.6 82.0 91.8 174.3 REMARK 620 6 HOH B 438 O 140.3 143.0 84.9 90.3 84.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO B 94 O REMARK 620 2 ASP B 170 OD1 173.8 REMARK 620 3 ASP B 170 OD2 121.7 52.1 REMARK 620 4 ASN B 172 OD1 77.2 98.3 67.5 REMARK 620 5 ASP B 173 OD1 76.5 102.0 78.9 115.5 REMARK 620 6 HOH B 429 O 114.5 71.0 114.2 160.0 83.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADP A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADP B 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5UJD RELATED DB: PDB REMARK 900 5UJD CONTAINS THE SAME PROTEIN WITH NO PRODUCT BOUND DBREF1 6NR6 A 1 254 UNP A0A166Q2C7_STAPS DBREF2 6NR6 A A0A166Q2C7 1 254 DBREF1 6NR6 B 1 254 UNP A0A166Q2C7_STAPS DBREF2 6NR6 B A0A166Q2C7 1 254 SEQADV 6NR6 ALA A 134 UNP A0A166Q2C VAL 134 CONFLICT SEQADV 6NR6 ALA A 139 UNP A0A166Q2C VAL 139 CONFLICT SEQADV 6NR6 VAL A 144 UNP A0A166Q2C ILE 144 CONFLICT SEQADV 6NR6 ALA B 134 UNP A0A166Q2C VAL 134 CONFLICT SEQADV 6NR6 ALA B 139 UNP A0A166Q2C VAL 139 CONFLICT SEQADV 6NR6 VAL B 144 UNP A0A166Q2C ILE 144 CONFLICT SEQRES 1 A 254 MET LYS GLN ILE TYR ASP THR LEU GLN LEU ILE PRO VAL SEQRES 2 A 254 ASP LYS ILE ASP LEU HIS GLU ALA PHE GLU PRO SER ARG SEQRES 3 A 254 LEU GLU LYS THR LYS GLU SER ILE ALA LYS GLU GLN HIS SEQRES 4 A 254 LEU ARG HIS PRO VAL LEU VAL VAL LYS THR LEU PHE GLY SEQRES 5 A 254 ARG TYR MET VAL ILE ASP GLY VAL HIS ARG PHE MET SER SEQRES 6 A 254 LEU LYS ALA LEU GLY CYS GLU VAL ILE PRO VAL GLN VAL SEQRES 7 A 254 ILE GLN ARG THR GLN TYR SER ILE GLY SER TRP HIS HIS SEQRES 8 A 254 LYS ILE PRO ASN GLY ALA TRP CYS GLU GLY LEU THR ASP SEQRES 9 A 254 GLU GLU LEU LEU PRO TRP THR THR GLU VAL ARG ASP GLU SEQRES 10 A 254 THR PRO PHE ILE THR MET CYS ASP GLN GLN THR GLU HIS SEQRES 11 A 254 TYR LEU TYR ALA ALA ASP LEU THR ALA ASP LYS LEU ASP SEQRES 12 A 254 VAL TRP LYS LYS VAL VAL ASN SER TYR SER ALA SER CYS SEQRES 13 A 254 ASN VAL GLU ARG VAL PRO HIS SER ALA CYS LEU CYS LEU SEQRES 14 A 254 ASP SER ASN ASP ILE LEU MET LYS TYR GLN PRO LEU GLN SEQRES 15 A 254 ILE GLY GLU ILE GLU ALA VAL VAL GLN ARG GLY GLN THR SEQRES 16 A 254 VAL PRO ALA GLY VAL THR ARG PHE ASN ILE ALA GLY ARG SEQRES 17 A 254 CYS LEU ASN LEU GLN VAL PRO LEU HIS LEU LEU LYS ASN SEQRES 18 A 254 SER ASN LEU GLY ASN GLN GLU GLN TRP HIS THR PHE LEU SEQRES 19 A 254 GLN LYS LYS ILE GLU SER MET ARG CYS TYR THR GLU LYS SEQRES 20 A 254 ILE TYR LEU ILE GLU ALA GLU SEQRES 1 B 254 MET LYS GLN ILE TYR ASP THR LEU GLN LEU ILE PRO VAL SEQRES 2 B 254 ASP LYS ILE ASP LEU HIS GLU ALA PHE GLU PRO SER ARG SEQRES 3 B 254 LEU GLU LYS THR LYS GLU SER ILE ALA LYS GLU GLN HIS SEQRES 4 B 254 LEU ARG HIS PRO VAL LEU VAL VAL LYS THR LEU PHE GLY SEQRES 5 B 254 ARG TYR MET VAL ILE ASP GLY VAL HIS ARG PHE MET SER SEQRES 6 B 254 LEU LYS ALA LEU GLY CYS GLU VAL ILE PRO VAL GLN VAL SEQRES 7 B 254 ILE GLN ARG THR GLN TYR SER ILE GLY SER TRP HIS HIS SEQRES 8 B 254 LYS ILE PRO ASN GLY ALA TRP CYS GLU GLY LEU THR ASP SEQRES 9 B 254 GLU GLU LEU LEU PRO TRP THR THR GLU VAL ARG ASP GLU SEQRES 10 B 254 THR PRO PHE ILE THR MET CYS ASP GLN GLN THR GLU HIS SEQRES 11 B 254 TYR LEU TYR ALA ALA ASP LEU THR ALA ASP LYS LEU ASP SEQRES 12 B 254 VAL TRP LYS LYS VAL VAL ASN SER TYR SER ALA SER CYS SEQRES 13 B 254 ASN VAL GLU ARG VAL PRO HIS SER ALA CYS LEU CYS LEU SEQRES 14 B 254 ASP SER ASN ASP ILE LEU MET LYS TYR GLN PRO LEU GLN SEQRES 15 B 254 ILE GLY GLU ILE GLU ALA VAL VAL GLN ARG GLY GLN THR SEQRES 16 B 254 VAL PRO ALA GLY VAL THR ARG PHE ASN ILE ALA GLY ARG SEQRES 17 B 254 CYS LEU ASN LEU GLN VAL PRO LEU HIS LEU LEU LYS ASN SEQRES 18 B 254 SER ASN LEU GLY ASN GLN GLU GLN TRP HIS THR PHE LEU SEQRES 19 B 254 GLN LYS LYS ILE GLU SER MET ARG CYS TYR THR GLU LYS SEQRES 20 B 254 ILE TYR LEU ILE GLU ALA GLU HET MG A 301 1 HET MG A 302 1 HET MG A 303 1 HET ADP A 304 26 HET MG B 301 1 HET MG B 302 1 HET ADP B 303 27 HETNAM MG MAGNESIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 3 MG 5(MG 2+) FORMUL 6 ADP 2(C10 H15 N5 O10 P2) FORMUL 10 HOH *187(H2 O) HELIX 1 AA1 GLN A 3 THR A 7 1 5 HELIX 2 AA2 GLU A 23 GLN A 38 1 16 HELIX 3 AA3 LEU A 50 GLY A 52 5 3 HELIX 4 AA4 GLY A 59 LEU A 69 1 11 HELIX 5 AA5 GLN A 80 THR A 82 5 3 HELIX 6 AA6 ASN A 95 TRP A 98 5 4 HELIX 7 AA7 CYS A 99 ASP A 104 1 6 HELIX 8 AA8 TYR A 133 LEU A 137 5 5 HELIX 9 AA9 ASP A 140 SER A 151 1 12 HELIX 10 AB1 GLN A 182 ARG A 192 1 11 HELIX 11 AB2 HIS A 217 LYS A 220 5 4 HELIX 12 AB3 GLY A 225 SER A 240 1 16 HELIX 13 AB4 LYS B 2 THR B 7 1 6 HELIX 14 AB5 GLU B 23 GLN B 38 1 16 HELIX 15 AB6 LEU B 50 GLY B 52 5 3 HELIX 16 AB7 GLY B 59 LEU B 69 1 11 HELIX 17 AB8 GLN B 80 THR B 82 5 3 HELIX 18 AB9 ASN B 95 TRP B 98 5 4 HELIX 19 AC1 CYS B 99 ASP B 104 1 6 HELIX 20 AC2 TYR B 133 LEU B 137 5 5 HELIX 21 AC3 ASP B 140 ALA B 154 1 15 HELIX 22 AC4 GLN B 182 ARG B 192 1 11 HELIX 23 AC5 HIS B 217 LYS B 220 5 4 HELIX 24 AC6 ASN B 221 GLY B 225 5 5 HELIX 25 AC7 ASN B 226 GLU B 239 1 14 SHEET 1 AA1 5 LEU A 8 PRO A 12 0 SHEET 2 AA1 5 VAL A 73 VAL A 78 -1 O VAL A 76 N GLN A 9 SHEET 3 AA1 5 VAL A 44 LYS A 48 1 N VAL A 44 O GLN A 77 SHEET 4 AA1 5 TYR A 54 ASP A 58 -1 O ILE A 57 N LEU A 45 SHEET 5 AA1 5 ILE A 16 ASP A 17 1 N ASP A 17 O TYR A 54 SHEET 1 AA2 2 HIS A 39 LEU A 40 0 SHEET 2 AA2 2 VAL A 214 PRO A 215 -1 O VAL A 214 N LEU A 40 SHEET 1 AA3 5 GLU A 129 LEU A 132 0 SHEET 2 AA3 5 ILE A 121 CYS A 124 -1 N MET A 123 O HIS A 130 SHEET 3 AA3 5 ILE A 174 TYR A 178 -1 O LEU A 175 N CYS A 124 SHEET 4 AA3 5 TYR A 84 ILE A 93 -1 N ILE A 93 O ILE A 174 SHEET 5 AA3 5 GLU A 159 PRO A 162 -1 O VAL A 161 N HIS A 90 SHEET 1 AA4 5 GLU A 129 LEU A 132 0 SHEET 2 AA4 5 ILE A 121 CYS A 124 -1 N MET A 123 O HIS A 130 SHEET 3 AA4 5 ILE A 174 TYR A 178 -1 O LEU A 175 N CYS A 124 SHEET 4 AA4 5 TYR A 84 ILE A 93 -1 N ILE A 93 O ILE A 174 SHEET 5 AA4 5 THR A 201 ILE A 205 -1 O ARG A 202 N GLY A 87 SHEET 1 AA5 5 LEU B 8 PRO B 12 0 SHEET 2 AA5 5 VAL B 73 VAL B 78 -1 O VAL B 76 N GLN B 9 SHEET 3 AA5 5 VAL B 44 LYS B 48 1 N VAL B 44 O GLN B 77 SHEET 4 AA5 5 TYR B 54 ASP B 58 -1 O ASP B 58 N LEU B 45 SHEET 5 AA5 5 ILE B 16 ASP B 17 1 N ASP B 17 O TYR B 54 SHEET 1 AA6 2 HIS B 39 LEU B 40 0 SHEET 2 AA6 2 VAL B 214 PRO B 215 -1 O VAL B 214 N LEU B 40 SHEET 1 AA7 2 TYR B 84 SER B 88 0 SHEET 2 AA7 2 THR B 201 ILE B 205 -1 O ARG B 202 N GLY B 87 SHEET 1 AA8 5 GLU B 129 LEU B 132 0 SHEET 2 AA8 5 ILE B 121 CYS B 124 -1 N MET B 123 O HIS B 130 SHEET 3 AA8 5 ILE B 174 TYR B 178 -1 O LYS B 177 N THR B 122 SHEET 4 AA8 5 HIS B 90 ILE B 93 -1 N ILE B 93 O ILE B 174 SHEET 5 AA8 5 GLU B 159 VAL B 161 -1 O VAL B 161 N HIS B 90 SSBOND 1 CYS A 99 CYS A 156 1555 1555 2.05 SSBOND 2 CYS A 166 CYS B 166 1555 1555 2.04 SSBOND 3 CYS A 168 CYS B 168 1555 1555 2.04 SSBOND 4 CYS B 99 CYS B 156 1555 1555 2.04 LINK OD1 ASP A 58 MG MG A 303 1555 1555 2.27 LINK O PRO A 94 MG MG A 301 1555 1555 2.41 LINK O GLY A 101 MG MG A 302 1555 1555 2.28 LINK OD1 ASP A 170 MG MG A 301 1555 1555 2.39 LINK OD2 ASP A 170 MG MG A 301 1555 1555 2.53 LINK OD1 ASN A 172 MG MG A 301 1555 1555 2.11 LINK OD2 ASP A 173 MG MG A 301 1555 1555 2.34 LINK MG MG A 301 O HOH A 480 1555 1555 2.38 LINK MG MG A 302 O HOH A 401 1555 1555 2.86 LINK MG MG A 302 O HOH A 417 1555 1555 2.41 LINK MG MG A 302 O HOH A 439 1555 1555 2.28 LINK MG MG A 302 O HOH A 531 1555 1555 2.53 LINK MG MG A 303 O1A ADP A 304 1555 1555 2.31 LINK MG MG A 303 O1B ADP A 304 1555 1555 2.16 LINK MG MG A 303 O HOH A 514 1555 1555 2.63 LINK OD1 ASP B 58 MG MG B 302 1555 1555 2.43 LINK O PRO B 94 MG MG B 301 1555 1555 2.44 LINK OD1 ASP B 170 MG MG B 301 1555 1555 2.50 LINK OD2 ASP B 170 MG MG B 301 1555 1555 2.52 LINK OD1 ASN B 172 MG MG B 301 1555 1555 2.39 LINK OD1 ASP B 173 MG MG B 301 1555 1555 2.30 LINK MG MG B 301 O HOH B 429 1555 1555 2.42 LINK MG MG B 302 O3B ADP B 303 1555 1555 2.57 LINK MG MG B 302 O2A ADP B 303 1555 1555 2.14 LINK MG MG B 302 O HOH B 414 1555 1555 2.48 LINK MG MG B 302 O HOH B 427 1555 1555 2.46 LINK MG MG B 302 O HOH B 438 1555 1555 2.28 SITE 1 AC1 5 PRO A 94 ASP A 170 ASN A 172 ASP A 173 SITE 2 AC1 5 HOH A 480 SITE 1 AC2 6 GLY A 101 ASP A 104 HOH A 401 HOH A 417 SITE 2 AC2 6 HOH A 439 HOH A 531 SITE 1 AC3 3 ASP A 58 ADP A 304 HOH A 514 SITE 1 AC4 9 ARG A 26 ASP A 58 GLY A 59 VAL A 60 SITE 2 AC4 9 HIS A 61 ARG A 62 ARG A 160 ARG A 242 SITE 3 AC4 9 MG A 303 SITE 1 AC5 5 PRO B 94 ASP B 170 ASN B 172 ASP B 173 SITE 2 AC5 5 HOH B 429 SITE 1 AC6 5 ASP B 58 ADP B 303 HOH B 414 HOH B 427 SITE 2 AC6 5 HOH B 438 SITE 1 AC7 15 ARG B 26 LYS B 29 THR B 30 SER B 33 SITE 2 AC7 15 ASP B 58 GLY B 59 VAL B 60 HIS B 61 SITE 3 AC7 15 ARG B 62 ARG B 242 TYR B 244 GLU B 252 SITE 4 AC7 15 MG B 302 HOH B 427 HOH B 438 CRYST1 101.644 73.074 88.372 90.00 90.00 90.00 P 21 21 2 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 0.009838 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013685 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011316 0.00000