HEADER TRANSPORT PROTEIN 12-JAN-15 4XKR TITLE CRYSTAL STRUCTURE OF NIKA FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH TITLE 2 NI-(L-HIS)(2-METHYL-THIAZOLIDINE DICARBOXYLATE) (CO-CRYSTALLIZATION TITLE 3 WITH NI(II) AND CDDELTAHIS MEDIUM SUPERNATANT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NICKEL ABC TRANSPORTER SUBSTRATE-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 19-491; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS USA300-ISMMS1; SOURCE 3 ORGANISM_TAXID: 1458279; SOURCE 4 GENE: AZ30_01190; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS EXTRACYTOPLASMIC NICKEL-BINDING PROTEIN, NICKEL IMPORT, ABC-TYPE KEYWDS 2 IMPORTER, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.LEBRETTE,C.CAVAZZA REVDAT 4 10-JAN-24 4XKR 1 LINK REVDAT 3 15-APR-15 4XKR 1 JRNL REVDAT 2 18-FEB-15 4XKR 1 JRNL REVDAT 1 11-FEB-15 4XKR 0 JRNL AUTH H.LEBRETTE,E.BOREZEE-DURANT,L.MARTIN,P.RICHAUD,E.BOERI ERBA, JRNL AUTH 2 C.CAVAZZA JRNL TITL NOVEL INSIGHTS INTO NICKEL IMPORT IN STAPHYLOCOCCUS AUREUS: JRNL TITL 2 THE POSITIVE ROLE OF FREE HISTIDINE AND STRUCTURAL JRNL TITL 3 CHARACTERIZATION OF A NEW THIAZOLIDINE-TYPE NICKEL CHELATOR. JRNL REF METALLOMICS V. 7 613 2015 JRNL REFN ESSN 1756-591X JRNL PMID 25611161 JRNL DOI 10.1039/C4MT00295D REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 47756 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2388 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 45.5588 - 4.4984 0.95 2821 149 0.1878 0.1967 REMARK 3 2 4.4984 - 3.5710 0.96 2717 142 0.1473 0.1666 REMARK 3 3 3.5710 - 3.1197 0.98 2726 143 0.1577 0.1965 REMARK 3 4 3.1197 - 2.8345 0.97 2690 142 0.1656 0.1990 REMARK 3 5 2.8345 - 2.6314 0.97 2700 142 0.1686 0.2106 REMARK 3 6 2.6314 - 2.4763 0.97 2671 141 0.1657 0.2029 REMARK 3 7 2.4763 - 2.3522 0.98 2700 142 0.1705 0.2201 REMARK 3 8 2.3522 - 2.2499 0.97 2660 140 0.1689 0.2269 REMARK 3 9 2.2499 - 2.1632 0.96 2632 138 0.1660 0.1911 REMARK 3 10 2.1632 - 2.0886 0.97 2670 141 0.1654 0.2106 REMARK 3 11 2.0886 - 2.0233 0.97 2636 139 0.1673 0.1765 REMARK 3 12 2.0233 - 1.9655 0.97 2676 141 0.1728 0.2114 REMARK 3 13 1.9655 - 1.9137 0.97 2629 138 0.1887 0.2317 REMARK 3 14 1.9137 - 1.8670 0.95 2583 136 0.2002 0.2582 REMARK 3 15 1.8670 - 1.8246 0.96 2600 137 0.2194 0.2387 REMARK 3 16 1.8246 - 1.7857 0.96 2625 138 0.2272 0.2542 REMARK 3 17 1.7857 - 1.7500 0.96 2632 139 0.2231 0.2376 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.330 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 : 0.008 3967 REMARK 3 ANGLE : 1.125 5343 REMARK 3 CHIRALITY : 0.053 586 REMARK 3 PLANARITY : 0.005 680 REMARK 3 DIHEDRAL : 14.377 1561 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 9 THROUGH 145 ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.7892 43.0686 11.6063 REMARK 3 T TENSOR REMARK 3 T11: 0.0882 T22: 0.1011 REMARK 3 T33: 0.1017 T12: 0.0021 REMARK 3 T13: 0.0174 T23: 0.0057 REMARK 3 L TENSOR REMARK 3 L11: 0.4504 L22: 0.9288 REMARK 3 L33: 0.6798 L12: -0.1603 REMARK 3 L13: -0.1011 L23: 0.3007 REMARK 3 S TENSOR REMARK 3 S11: -0.0209 S12: -0.0003 S13: -0.0479 REMARK 3 S21: 0.0130 S22: -0.0088 S23: 0.0571 REMARK 3 S31: 0.0207 S32: -0.0236 S33: -0.0003 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 146 THROUGH 230 ) REMARK 3 ORIGIN FOR THE GROUP (A): 48.2223 57.4691 28.9519 REMARK 3 T TENSOR REMARK 3 T11: 0.1037 T22: 0.1221 REMARK 3 T33: 0.0747 T12: 0.0136 REMARK 3 T13: -0.0127 T23: -0.0066 REMARK 3 L TENSOR REMARK 3 L11: 0.6494 L22: 0.6305 REMARK 3 L33: 0.7103 L12: -0.2158 REMARK 3 L13: 0.1232 L23: -0.0900 REMARK 3 S TENSOR REMARK 3 S11: -0.0889 S12: -0.0913 S13: 0.0140 REMARK 3 S21: 0.2383 S22: 0.0672 S23: -0.0084 REMARK 3 S31: -0.0293 S32: 0.0933 S33: -0.0479 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 231 THROUGH 280 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.5066 75.4192 7.2556 REMARK 3 T TENSOR REMARK 3 T11: 0.0971 T22: 0.0854 REMARK 3 T33: 0.1245 T12: -0.0201 REMARK 3 T13: -0.0102 T23: 0.0046 REMARK 3 L TENSOR REMARK 3 L11: 0.1268 L22: 0.5278 REMARK 3 L33: 0.5277 L12: -0.1214 REMARK 3 L13: -0.0691 L23: 0.0329 REMARK 3 S TENSOR REMARK 3 S11: -0.0348 S12: 0.0873 S13: 0.1008 REMARK 3 S21: -0.0166 S22: -0.0140 S23: -0.0312 REMARK 3 S31: -0.0882 S32: 0.0361 S33: 0.0102 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 281 THROUGH 314 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.8382 81.6525 1.2043 REMARK 3 T TENSOR REMARK 3 T11: 0.1945 T22: 0.1390 REMARK 3 T33: 0.1900 T12: -0.0211 REMARK 3 T13: 0.0022 T23: 0.0388 REMARK 3 L TENSOR REMARK 3 L11: 0.2174 L22: 0.6573 REMARK 3 L33: 0.7470 L12: 0.1660 REMARK 3 L13: -0.0377 L23: 0.3490 REMARK 3 S TENSOR REMARK 3 S11: 0.0027 S12: 0.0136 S13: 0.2335 REMARK 3 S21: -0.3683 S22: 0.1019 S23: -0.0627 REMARK 3 S31: -0.1602 S32: 0.0677 S33: 0.2150 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 315 THROUGH 365 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.7920 76.0723 16.5743 REMARK 3 T TENSOR REMARK 3 T11: 0.1142 T22: 0.1046 REMARK 3 T33: 0.1213 T12: -0.0056 REMARK 3 T13: -0.0046 T23: -0.0069 REMARK 3 L TENSOR REMARK 3 L11: 0.2809 L22: 0.1546 REMARK 3 L33: 0.5002 L12: -0.0111 REMARK 3 L13: -0.1759 L23: 0.2057 REMARK 3 S TENSOR REMARK 3 S11: 0.0043 S12: -0.0734 S13: 0.0607 REMARK 3 S21: 0.1786 S22: 0.0254 S23: 0.0554 REMARK 3 S31: -0.0669 S32: -0.0769 S33: 0.0035 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 366 THROUGH 472 ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.5695 60.9267 5.5522 REMARK 3 T TENSOR REMARK 3 T11: 0.0871 T22: 0.1060 REMARK 3 T33: 0.0975 T12: -0.0087 REMARK 3 T13: 0.0038 T23: -0.0067 REMARK 3 L TENSOR REMARK 3 L11: 0.4586 L22: 0.7788 REMARK 3 L33: 0.3067 L12: -0.2343 REMARK 3 L13: -0.1108 L23: -0.0085 REMARK 3 S TENSOR REMARK 3 S11: -0.0121 S12: 0.0532 S13: 0.0078 REMARK 3 S21: -0.0622 S22: -0.0046 S23: -0.0546 REMARK 3 S31: -0.0277 S32: 0.0240 S33: 0.0015 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 4XKR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000205848. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47766 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 45.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07800 REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.61600 REMARK 200 FOR SHELL : 3.360 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: 4OFJ REMARK 200 REMARK 200 REMARK: PLATE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27% PEG 3350, 0.1 M HEPES PH 7.0 - REMARK 280 PROTEIN PRE-INCUBATED WITH NICL2 AND CDDELTAHIS MEDIUM REMARK 280 SUPERNATANT., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 30.90150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.78300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.68650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.78300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.90150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.68650 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL 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 CYS A 1 REMARK 465 GLY A 2 REMARK 465 SER A 3 REMARK 465 MET A 4 REMARK 465 HIS A 5 REMARK 465 SER A 6 REMARK 465 SER A 7 REMARK 465 GLY A 8 REMARK 465 ARG A 473 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 O HOH A 681 O HOH A 699 4465 2.16 REMARK 500 O HOH A 621 O HOH A 627 4565 2.17 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 LEU A 17 67.54 66.50 REMARK 500 LYS A 20 -94.34 -99.16 REMARK 500 ALA A 51 -72.40 -117.90 REMARK 500 LYS A 143 55.86 -90.25 REMARK 500 ARG A 165 -59.05 -129.77 REMARK 500 THR A 277 -72.06 -126.23 REMARK 500 ILE A 374 75.98 -159.37 REMARK 500 ILE A 462 -51.34 -127.74 REMARK 500 LEU A 464 -55.63 -150.59 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 NA A 523 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 355 OE2 REMARK 620 2 GOL A 522 O3 108.2 REMARK 620 3 HOH A 813 O 114.9 97.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 501 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 502 ND1 REMARK 620 2 HIS A 502 N 88.6 REMARK 620 3 HIS A 502 O 90.9 81.6 REMARK 620 4 41K A 503 N 94.9 95.9 173.6 REMARK 620 5 41K A 503 OXT 95.9 175.3 96.8 85.1 REMARK 620 6 41K A 503 OAA 176.9 94.0 91.2 83.0 81.6 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 NI A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HIS A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 41K A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 513 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 514 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 515 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 516 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 517 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 518 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 519 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 520 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 521 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 522 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 523 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OFJ RELATED DB: PDB REMARK 900 THE SAME PROTEIN CO-PURIFIED WITH NI(L-HIS)2 REMARK 900 RELATED ID: 4XKN RELATED DB: PDB REMARK 900 THE SAME PROTEIN, CO-CRYSTALLIZATION WITH NI(II) AND L-HISTIDINE REMARK 900 RELATED ID: 4XKP RELATED DB: PDB REMARK 900 THE SAME PROTEIN, CO-CRYSTALLIZATION WITH NI(II) AND BHI MEDIUM REMARK 900 SUPERNATANT REMARK 900 RELATED ID: 4XKQ RELATED DB: PDB REMARK 900 THE SAME PROTEIN, CO-CRYSTALLIZATION WITH NI(II) AND CD MEDIUM REMARK 900 SUPERNATANT DBREF 4XKR A 1 473 UNP W6DY02 W6DY02_STAAU 19 491 SEQRES 1 A 473 CYS GLY SER MET HIS SER SER GLY LYS ASP LEU ASN ILE SEQRES 2 A 473 SER LEU PRO LEU LYS THR LYS SER ILE ALA PRO TYR GLU SEQRES 3 A 473 THR ASP VAL PRO VAL LYS ILE GLY ALA ALA GLU SER LEU SEQRES 4 A 473 PHE LYS THR ASN ASP GLN GLY LYS ILE GLU LYS ALA LEU SEQRES 5 A 473 VAL LYS SER TYR HIS GLN PRO ASN ASP THR THR LEU ASP SEQRES 6 A 473 ILE GLU LEU LYS ASP ASN ILE LYS PHE GLN ASN GLY GLN SEQRES 7 A 473 LYS LEU THR ALA GLU LYS VAL LYS SER SER LEU GLU ASN SEQRES 8 A 473 SER MET LYS LYS SER ASP LEU VAL LYS TYR SER LEU PRO SEQRES 9 A 473 ILE SER SER ILE THR ALA LYS GLY GLN LYS LEU THR ILE SEQRES 10 A 473 LYS THR ASN SER ALA TYR PRO GLU LEU VAL SER GLU LEU SEQRES 11 A 473 ALA ASN PRO PHE MET ALA ILE TYR ASP THR ASP ALA LYS SEQRES 12 A 473 SER ASP VAL ASN GLN THR PRO VAL GLY THR GLY PRO TYR SEQRES 13 A 473 GLN ILE LYS ASP TYR LYS GLN SER ARG LYS ILE SER LEU SEQRES 14 A 473 SER ASN PHE LYS ASP TYR TRP GLN GLY LYS PRO LYS LEU SEQRES 15 A 473 ASP HIS ILE THR VAL THR TYR GLN GLU ASP GLY ASN ASN SEQRES 16 A 473 ARG VAL ARG ASN LEU GLU SER GLN LYS ASP ASP LEU ILE SEQRES 17 A 473 THR ASP VAL PRO VAL ASN LYS VAL GLN ASP ILE GLU ASN SEQRES 18 A 473 ASN GLN ASN LEU LYS VAL SER LYS GLU SER GLY PHE ARG SEQRES 19 A 473 THR SER LEU LEU MET TYR ASN HIS THR ASN LYS LYS MET SEQRES 20 A 473 THR LYS SER VAL ARG GLU ALA LEU ASP HIS ILE ILE ASP SEQRES 21 A 473 ARG GLN GLY ILE ALA ASP HIS ILE TYR GLN GLY TYR ALA SEQRES 22 A 473 LYS PRO ALA THR SER PRO PHE ASN ASP LYS ILE PRO TYR SEQRES 23 A 473 ILE LYS GLU PRO LYS LEU THR LYS GLN ASN ILE GLU GLN SEQRES 24 A 473 ALA LYS MET LEU LEU ALA LYS ASP GLY TYR THR LYS GLU SEQRES 25 A 473 HIS PRO LEU LYS ILE LYS LEU ILE THR TYR ASP GLY ARG SEQRES 26 A 473 PRO GLU LEU SER LYS ILE ALA GLN VAL LEU GLN SER ASP SEQRES 27 A 473 ALA LYS LYS ALA ASN ILE GLU ILE ASP ILE LYS SER VAL SEQRES 28 A 473 ASP ASP ILE GLU GLY TYR LEU LYS ASP ARG SER ALA TRP SEQRES 29 A 473 ASP ALA THR MET TYR SER PHE GLY THR ILE PRO ARG GLY SEQRES 30 A 473 ASP THR GLY TYR PHE PHE ASN GLN ALA TYR LYS LYS ASP SEQRES 31 A 473 GLY ALA ILE ASN LYS GLY ASP TYR ASN ASN SER ASN VAL SEQRES 32 A 473 ASP ASP LEU ILE ASN GLN LEU ASN HIS THR VAL ASP VAL SEQRES 33 A 473 LYS GLU ARG HIS ASN ILE SER ASN ASP ILE ILE LYS LEU SEQRES 34 A 473 SER SER ARG ASP VAL PRO ASN SER TYR ILE ALA TYR ASN SEQRES 35 A 473 ASP GLN ILE VAL ALA ALA ASN SER LYS VAL LYS ASN TYR SEQRES 36 A 473 LYS VAL THR PRO GLU GLY ILE TYR LEU ILE ASP TYR ARG SEQRES 37 A 473 THR THR ILE GLU ARG HET NI A 501 1 HET HIS A 502 11 HET 41K A 503 12 HET EPE A 504 15 HET GOL A 505 6 HET GOL A 506 6 HET GOL A 507 6 HET GOL A 508 6 HET GOL A 509 6 HET GOL A 510 6 HET GOL A 511 6 HET GOL A 512 6 HET GOL A 513 6 HET GOL A 514 6 HET GOL A 515 6 HET GOL A 516 6 HET GOL A 517 6 HET GOL A 518 6 HET GOL A 519 6 HET GOL A 520 6 HET GOL A 521 6 HET GOL A 522 6 HET NA A 523 1 HETNAM NI NICKEL (II) ION HETNAM HIS HISTIDINE HETNAM 41K (2R,4R)-2-METHYL-1,3-THIAZOLIDINE-2,4-DICARBOXYLIC ACID HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN EPE HEPES HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NI NI 2+ FORMUL 3 HIS C6 H10 N3 O2 1+ FORMUL 4 41K C6 H9 N O4 S FORMUL 5 EPE C8 H18 N2 O4 S FORMUL 6 GOL 18(C3 H8 O3) FORMUL 24 NA NA 1+ FORMUL 25 HOH *523(H2 O) HELIX 1 AA1 ASP A 28 ILE A 33 1 6 HELIX 2 AA2 THR A 81 SER A 96 1 16 HELIX 3 AA3 SER A 96 LEU A 103 1 8 HELIX 4 AA4 GLU A 125 LEU A 130 1 6 HELIX 5 AA5 ALA A 131 ALA A 136 5 6 HELIX 6 AA6 ASP A 192 SER A 202 1 11 HELIX 7 AA7 PRO A 212 ASN A 214 5 3 HELIX 8 AA8 LYS A 215 ASN A 222 1 8 HELIX 9 AA9 THR A 248 ILE A 259 1 12 HELIX 10 AB1 ASP A 260 ILE A 268 1 9 HELIX 11 AB2 ASN A 296 LYS A 306 1 11 HELIX 12 AB3 GLU A 327 ALA A 342 1 16 HELIX 13 AB4 ASP A 353 LYS A 359 1 7 HELIX 14 AB5 THR A 379 TYR A 387 1 9 HELIX 15 AB6 ASN A 400 HIS A 412 1 13 HELIX 16 AB7 ASP A 415 VAL A 434 1 20 SHEET 1 AA1 7 TYR A 156 LYS A 162 0 SHEET 2 AA1 7 LYS A 166 ASN A 171 -1 O SER A 168 N LYS A 159 SHEET 3 AA1 7 HIS A 184 TYR A 189 -1 O VAL A 187 N ILE A 167 SHEET 4 AA1 7 ASP A 10 LEU A 15 1 N ILE A 13 O THR A 186 SHEET 5 AA1 7 LEU A 207 ILE A 208 1 O LEU A 207 N SER A 14 SHEET 6 AA1 7 GLN A 444 ASN A 449 -1 O ALA A 447 N ILE A 208 SHEET 7 AA1 7 LEU A 225 GLU A 230 -1 N SER A 228 O VAL A 446 SHEET 1 AA2 2 PHE A 40 THR A 42 0 SHEET 2 AA2 2 ILE A 48 LYS A 50 -1 O GLU A 49 N LYS A 41 SHEET 1 AA3 4 VAL A 53 ASN A 60 0 SHEET 2 AA3 4 THR A 63 LEU A 68 -1 O GLU A 67 N SER A 55 SHEET 3 AA3 4 LYS A 114 LYS A 118 -1 O LEU A 115 N ILE A 66 SHEET 4 AA3 4 SER A 107 LYS A 111 -1 N SER A 107 O LYS A 118 SHEET 1 AA4 6 ALA A 273 PRO A 275 0 SHEET 2 AA4 6 ASN A 436 ASN A 442 -1 O TYR A 441 N LYS A 274 SHEET 3 AA4 6 ARG A 234 TYR A 240 -1 N LEU A 238 O SER A 437 SHEET 4 AA4 6 ALA A 366 GLY A 372 -1 O THR A 367 N MET A 239 SHEET 5 AA4 6 LEU A 315 THR A 321 1 N ILE A 320 O MET A 368 SHEET 6 AA4 6 ILE A 344 SER A 350 1 O GLU A 345 N LEU A 315 SHEET 1 AA5 2 VAL A 452 LYS A 453 0 SHEET 2 AA5 2 THR A 470 ILE A 471 -1 O THR A 470 N LYS A 453 LINK OE2 GLU A 355 NA NA A 523 1555 1555 2.83 LINK NI NI A 501 ND1 HIS A 502 1555 1555 2.09 LINK NI NI A 501 N HIS A 502 1555 1555 2.07 LINK NI NI A 501 O HIS A 502 1555 1555 2.07 LINK NI NI A 501 N 41K A 503 1555 1555 2.13 LINK NI NI A 501 OXT 41K A 503 1555 1555 2.13 LINK NI NI A 501 OAA 41K A 503 1555 1555 1.99 LINK O3 GOL A 522 NA NA A 523 1555 1555 2.65 LINK NA NA A 523 O HOH A 813 1555 1555 2.72 SITE 1 AC1 2 HIS A 502 41K A 503 SITE 1 AC2 11 LEU A 17 ARG A 234 TYR A 322 ARG A 325 SITE 2 AC2 11 GLU A 355 TYR A 369 SER A 370 NI A 501 SITE 3 AC2 11 41K A 503 NA A 523 HOH A 773 SITE 1 AC3 15 ASP A 28 PHE A 134 ARG A 234 TYR A 369 SITE 2 AC3 15 SER A 370 PHE A 371 GLY A 372 ILE A 393 SITE 3 AC3 15 NI A 501 HIS A 502 NA A 523 HOH A 752 SITE 4 AC3 15 HOH A 784 HOH A 836 HOH A 846 SITE 1 AC4 12 ILE A 48 GLU A 49 LYS A 50 TYR A 56 SITE 2 AC4 12 TYR A 101 LYS A 389 ASP A 390 ASP A 404 SITE 3 AC4 12 GOL A 508 HOH A 645 HOH A 676 HOH A 961 SITE 1 AC5 6 LYS A 159 LYS A 318 LYS A 349 TYR A 357 SITE 2 AC5 6 HOH A 610 HOH A 986 SITE 1 AC6 9 LYS A 32 LYS A 456 GLY A 461 ILE A 462 SITE 2 AC6 9 TYR A 463 HOH A 759 HOH A 786 HOH A 840 SITE 3 AC6 9 HOH A 990 SITE 1 AC7 9 GLU A 83 ALA A 110 GLN A 295 ILE A 297 SITE 2 AC7 9 ASP A 338 GOL A 521 HOH A 625 HOH A 644 SITE 3 AC7 9 HOH A 668 SITE 1 AC8 6 TYR A 101 ASN A 384 LYS A 388 LYS A 389 SITE 2 AC8 6 EPE A 504 HOH A 845 SITE 1 AC9 8 ASP A 260 GLY A 263 ILE A 264 HIS A 267 SITE 2 AC9 8 VAL A 334 HOH A 800 HOH A 815 HOH A1046 SITE 1 AD1 5 GLU A 90 SER A 106 ILE A 108 HOH A 673 SITE 2 AD1 5 HOH A 818 SITE 1 AD2 10 SER A 55 GLU A 67 ARG A 252 TYR A 398 SITE 2 AD2 10 ASN A 399 ASN A 400 ASP A 433 GOL A 518 SITE 3 AD2 10 HOH A 602 HOH A 612 SITE 1 AD3 10 ASP A 256 ARG A 261 THR A 277 PRO A 290 SITE 2 AD3 10 LYS A 291 THR A 293 SER A 431 HOH A 742 SITE 3 AD3 10 HOH A 772 HOH A 798 SITE 1 AD4 8 GLN A 58 ASN A 60 ASP A 61 THR A 63 SITE 2 AD4 8 THR A 119 ALA A 122 TYR A 123 HOH A 771 SITE 1 AD5 7 THR A 149 LYS A 159 ILE A 348 LYS A 349 SITE 2 AD5 7 SER A 350 HOH A 619 HOH A 666 SITE 1 AD6 7 TYR A 463 HOH A 749 HOH A 826 HOH A 855 SITE 2 AD6 7 HOH A 869 HOH A 889 HOH A 910 SITE 1 AD7 5 LYS A 226 LYS A 453 ASN A 454 TYR A 455 SITE 2 AD7 5 HOH A1007 SITE 1 AD8 4 LYS A 143 VAL A 351 ASP A 352 ASP A 353 SITE 1 AD9 10 LYS A 114 HIS A 242 LYS A 245 MET A 247 SITE 2 AD9 10 THR A 248 ARG A 252 GOL A 511 HOH A 602 SITE 3 AD9 10 HOH A 675 HOH A 681 SITE 1 AE1 7 LYS A 54 LYS A 69 ASP A 70 ASN A 71 SITE 2 AE1 7 ASN A 402 HOH A 632 HOH A 957 SITE 1 AE2 6 THR A 109 ALA A 110 LYS A 114 LEU A 115 SITE 2 AE2 6 THR A 116 LYS A 245 SITE 1 AE3 7 GLU A 83 LYS A 86 THR A 109 ALA A 110 SITE 2 AE3 7 GLU A 298 LYS A 341 GOL A 507 SITE 1 AE4 8 PHE A 134 ALA A 392 LYS A 395 NA A 523 SITE 2 AE4 8 HOH A 820 HOH A 893 HOH A 940 HOH A 969 SITE 1 AE5 5 GLU A 355 HIS A 502 41K A 503 GOL A 522 SITE 2 AE5 5 HOH A 813 CRYST1 61.803 67.373 115.566 90.00 90.00 90.00 P 21 21 21 4 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 0.016180 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014843 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008653 0.00000