HEADER TRANSPORT PROTEIN 15-JAN-14 4OFL TITLE CRYSTAL STRUCTURE OF YNTA FROM YERSINIA PESTIS IN COMPLEX WITH NI(L- TITLE 2 HIS)2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXTRACYTOPLASMIC NICKEL-BINDING PROTEIN YPYNTA; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PUTATIVE SUBSTRATE-BINDING PERIPLASMIC PROTEIN OF ABC COMPND 5 TRANSPORTER, YPYNTA; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PESTIS; SOURCE 3 ORGANISM_TAXID: 632; SOURCE 4 GENE: OPPA4, Y1231, YP_2461, YPO2660; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NICKEL IMPORT, PERIPLASMIC, ABC-TYPE IMPORTER, EXTRACYTOPLASMIC KEYWDS 2 NICKEL-BINDING PROTEIN, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.LEBRETTE,C.CAVAZZA REVDAT 4 16-OCT-24 4OFL 1 REMARK REVDAT 3 20-SEP-23 4OFL 1 REMARK LINK REVDAT 2 19-NOV-14 4OFL 1 JRNL REVDAT 1 01-OCT-14 4OFL 0 JRNL AUTH H.LEBRETTE,C.BROCHIER-ARMANET,B.ZAMBELLI,H.DE REUSE, JRNL AUTH 2 E.BOREZEE-DURANT,S.CIURLI,C.CAVAZZA JRNL TITL PROMISCUOUS NICKEL IMPORT IN HUMAN PATHOGENS: STRUCTURE, JRNL TITL 2 THERMODYNAMICS, AND EVOLUTION OF EXTRACYTOPLASMIC JRNL TITL 3 NICKEL-BINDING PROTEINS. JRNL REF STRUCTURE V. 22 1421 2014 JRNL REFN ISSN 0969-2126 JRNL PMID 25199691 JRNL DOI 10.1016/J.STR.2014.07.012 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 26600 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1331 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 46.4582 - 5.8133 0.93 2497 132 0.1715 0.2004 REMARK 3 2 5.8133 - 4.6156 0.94 2489 131 0.1679 0.1891 REMARK 3 3 4.6156 - 4.0325 0.95 2518 133 0.1530 0.1774 REMARK 3 4 4.0325 - 3.6640 0.97 2558 134 0.1737 0.2066 REMARK 3 5 3.6640 - 3.4014 0.94 2488 131 0.2103 0.2391 REMARK 3 6 3.4014 - 3.2009 0.96 2553 135 0.2140 0.3124 REMARK 3 7 3.2009 - 3.0407 0.96 2546 134 0.2421 0.3245 REMARK 3 8 3.0407 - 2.9083 0.97 2526 133 0.2547 0.2989 REMARK 3 9 2.9083 - 2.7964 0.97 2579 135 0.2515 0.3146 REMARK 3 10 2.7964 - 2.6999 0.95 2515 133 0.2572 0.3518 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.770 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 : 0.009 7998 REMARK 3 ANGLE : 0.783 10888 REMARK 3 CHIRALITY : 0.031 1160 REMARK 3 PLANARITY : 0.004 1422 REMARK 3 DIHEDRAL : 12.759 2848 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 3 THROUGH 115 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.4150 0.7056 44.9806 REMARK 3 T TENSOR REMARK 3 T11: 0.6757 T22: 0.3401 REMARK 3 T33: 0.4977 T12: 0.1680 REMARK 3 T13: -0.0972 T23: -0.0517 REMARK 3 L TENSOR REMARK 3 L11: 1.9020 L22: 2.2136 REMARK 3 L33: 1.9487 L12: -0.8156 REMARK 3 L13: 1.0221 L23: 0.2619 REMARK 3 S TENSOR REMARK 3 S11: 0.2371 S12: 0.0390 S13: -0.1419 REMARK 3 S21: 0.2398 S22: -0.0041 S23: -0.4550 REMARK 3 S31: 0.6666 S32: 0.4591 S33: -0.1652 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 116 THROUGH 152 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.6534 0.3295 41.2867 REMARK 3 T TENSOR REMARK 3 T11: 0.6823 T22: 0.3829 REMARK 3 T33: 0.4965 T12: 0.1422 REMARK 3 T13: -0.0598 T23: -0.0401 REMARK 3 L TENSOR REMARK 3 L11: 2.3713 L22: 4.1185 REMARK 3 L33: 3.8208 L12: -0.7389 REMARK 3 L13: -1.0423 L23: 2.6071 REMARK 3 S TENSOR REMARK 3 S11: 0.2918 S12: 0.3589 S13: 0.2228 REMARK 3 S21: -0.4605 S22: 0.2814 S23: -0.5644 REMARK 3 S31: 0.5578 S32: 0.7816 S33: -0.5684 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 153 THROUGH 455 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.0798 29.0066 44.4543 REMARK 3 T TENSOR REMARK 3 T11: 0.1764 T22: 0.2362 REMARK 3 T33: 0.1924 T12: 0.0484 REMARK 3 T13: 0.0070 T23: -0.0209 REMARK 3 L TENSOR REMARK 3 L11: 1.7102 L22: 1.2408 REMARK 3 L33: 1.1549 L12: 0.9943 REMARK 3 L13: 0.5113 L23: 0.1659 REMARK 3 S TENSOR REMARK 3 S11: 0.1087 S12: -0.0012 S13: 0.1148 REMARK 3 S21: 0.0034 S22: -0.1646 S23: 0.1463 REMARK 3 S31: 0.1085 S32: 0.0327 S33: 0.0492 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 456 THROUGH 498 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.2617 18.6686 38.4875 REMARK 3 T TENSOR REMARK 3 T11: 0.3011 T22: 0.2440 REMARK 3 T33: 0.2625 T12: -0.0486 REMARK 3 T13: 0.0643 T23: -0.0155 REMARK 3 L TENSOR REMARK 3 L11: 2.3686 L22: 3.0354 REMARK 3 L33: 1.9226 L12: 1.0593 REMARK 3 L13: 1.2362 L23: 0.4858 REMARK 3 S TENSOR REMARK 3 S11: -0.0787 S12: 0.1868 S13: -0.2891 REMARK 3 S21: -0.3786 S22: 0.0395 S23: 0.1174 REMARK 3 S31: 0.4207 S32: 0.0273 S33: 0.0167 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 3 THROUGH 115 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.5601 87.0175 26.8920 REMARK 3 T TENSOR REMARK 3 T11: 0.7298 T22: 0.3466 REMARK 3 T33: 0.5840 T12: -0.0290 REMARK 3 T13: 0.0163 T23: 0.0732 REMARK 3 L TENSOR REMARK 3 L11: 2.6439 L22: 3.2423 REMARK 3 L33: 2.7779 L12: 0.4919 REMARK 3 L13: 1.3946 L23: -1.3926 REMARK 3 S TENSOR REMARK 3 S11: -0.2152 S12: 0.5127 S13: 0.5241 REMARK 3 S21: -0.5298 S22: -0.0223 S23: 0.0373 REMARK 3 S31: -0.5438 S32: 0.3741 S33: 0.3083 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 116 THROUGH 152 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.5674 86.7633 24.2907 REMARK 3 T TENSOR REMARK 3 T11: 0.6804 T22: 0.5531 REMARK 3 T33: 0.5282 T12: -0.0317 REMARK 3 T13: 0.1213 T23: 0.2125 REMARK 3 L TENSOR REMARK 3 L11: 1.7600 L22: 1.9355 REMARK 3 L33: 4.4215 L12: -0.4887 REMARK 3 L13: 1.3264 L23: 0.8191 REMARK 3 S TENSOR REMARK 3 S11: -0.1730 S12: 0.6627 S13: 0.3028 REMARK 3 S21: -0.6704 S22: -0.0450 S23: -0.5812 REMARK 3 S31: -0.5712 S32: 1.0847 S33: 0.2330 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 153 THROUGH 455 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.1915 58.9014 25.8296 REMARK 3 T TENSOR REMARK 3 T11: 0.2348 T22: 0.2556 REMARK 3 T33: 0.4696 T12: 0.0427 REMARK 3 T13: 0.0250 T23: 0.0566 REMARK 3 L TENSOR REMARK 3 L11: 0.5629 L22: 2.3633 REMARK 3 L33: 2.0408 L12: 0.6448 REMARK 3 L13: 0.3766 L23: 1.1882 REMARK 3 S TENSOR REMARK 3 S11: 0.0950 S12: 0.0351 S13: 0.2193 REMARK 3 S21: -0.0828 S22: -0.0588 S23: -0.4462 REMARK 3 S31: -0.1667 S32: 0.0191 S33: -0.0196 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 456 THROUGH 498 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.8403 69.8395 41.2226 REMARK 3 T TENSOR REMARK 3 T11: 0.3516 T22: 0.2310 REMARK 3 T33: 0.4297 T12: -0.0265 REMARK 3 T13: -0.0063 T23: -0.0249 REMARK 3 L TENSOR REMARK 3 L11: 1.8836 L22: 3.0064 REMARK 3 L33: 2.2864 L12: 0.5500 REMARK 3 L13: 0.7972 L23: 1.3061 REMARK 3 S TENSOR REMARK 3 S11: 0.0920 S12: -0.1289 S13: 0.3855 REMARK 3 S21: 0.3517 S22: -0.0346 S23: -0.0456 REMARK 3 S31: -0.2735 S32: 0.0486 S33: -0.0902 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 2 REMARK 3 NCS GROUP : 1 REMARK 3 NCS GROUP : 2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : NULL REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4OFL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084430. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 8.5 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) : 0.98400 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26613 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 46.451 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 10.5400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.51200 REMARK 200 FOR SHELL : 2.140 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: PDB ENTRY 3RY3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 29 % PEG 10K , 50 MM TRIS PH 8.5, 1 M REMARK 280 NACL + NICL2 + L-HIS, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K 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 106.91500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 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 ALA A 1 REMARK 465 THR A 2 REMARK 465 GLN A 499 REMARK 465 ALA B 1 REMARK 465 THR B 2 REMARK 465 GLN B 499 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 PHE A 17 56.70 -110.01 REMARK 500 LYS A 95 -131.46 54.45 REMARK 500 VAL A 96 84.11 51.91 REMARK 500 LEU A 102 -63.96 -104.20 REMARK 500 SER A 129 -52.84 -125.30 REMARK 500 GLN A 162 -76.30 -111.97 REMARK 500 TRP A 385 -155.64 -149.61 REMARK 500 GLU A 405 -124.14 50.73 REMARK 500 ASN A 408 60.89 37.28 REMARK 500 THR A 445 -56.45 -121.74 REMARK 500 PHE B 17 57.61 -107.34 REMARK 500 LYS B 95 -131.66 53.36 REMARK 500 VAL B 96 87.26 48.46 REMARK 500 LEU B 102 -61.19 -104.24 REMARK 500 SER B 129 -51.21 -125.93 REMARK 500 HIS B 279 32.64 -96.16 REMARK 500 TRP B 385 -155.55 -149.89 REMARK 500 GLU B 405 -124.17 49.59 REMARK 500 ASN B 408 62.23 38.23 REMARK 500 THR B 445 -56.13 -121.70 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 NI A 501 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 482 NE2 REMARK 620 2 HIS A 502 N 88.3 REMARK 620 3 HIS A 502 ND1 166.2 80.0 REMARK 620 4 HIS A 502 OXT 94.8 79.9 90.4 REMARK 620 5 HIS A 503 O 89.6 84.4 82.0 163.6 REMARK 620 6 HIS A 503 ND1 88.6 175.2 103.5 96.6 99.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 501 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 482 NE2 REMARK 620 2 HIS B 502 N 80.3 REMARK 620 3 HIS B 502 OXT 86.4 86.4 REMARK 620 4 HIS B 502 ND1 163.5 84.8 85.5 REMARK 620 5 HIS B 503 ND1 74.6 154.9 92.0 120.0 REMARK 620 6 HIS B 503 O 95.2 98.0 175.6 94.0 84.4 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 HIS A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HIS B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HIS B 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OFO RELATED DB: PDB REMARK 900 THE SAME PROTEIN, UNLIGANDED FORM DBREF 4OFL A 1 499 UNP Q7CJS8 Q7CJS8_YERPE 27 525 DBREF 4OFL B 1 499 UNP Q7CJS8 Q7CJS8_YERPE 27 525 SEQRES 1 A 499 ALA THR HIS THR LEU GLN LEU ALA ILE GLY ASP GLU PRO SEQRES 2 A 499 THR GLU GLY PHE ASP PRO MET LEU GLY TRP SER HIS GLY SEQRES 3 A 499 SER TYR LEU LEU LEU HIS SER PRO LEU LEU LYS GLN ASN SEQRES 4 A 499 GLU ASP PHE SER TRP ASP SER LEU LEU LEU SER GLN TYR SEQRES 5 A 499 GLN PRO SER ASP ASP GLY LYS THR TRP LEU LEU THR LEU SEQRES 6 A 499 LYS PRO ASP LEU LYS PHE SER ASP GLY SER PRO LEU THR SEQRES 7 A 499 ALA LYS ASP VAL ALA PHE THR TYR ASN ASN ALA ALA ALA SEQRES 8 A 499 SER GLY GLY LYS VAL ASP MET GLY ASN PHE LEU SER ALA SEQRES 9 A 499 GLU VAL ILE ASP PRO LEU ASN VAL ARG ILE HIS LEU LYS SEQRES 10 A 499 ALA PRO GLN SER THR PHE VAL ASN VAL LEU GLY SER LEU SEQRES 11 A 499 GLY ILE VAL SER ALA ASP LYS TYR ASN ALA LYS THR TYR SEQRES 12 A 499 ALA GLN LYS PRO ILE GLY ALA GLY PRO TYR ARG LEU VAL SEQRES 13 A 499 SER PHE GLN PRO GLY GLN GLN MET ILE VAL GLU ALA ASN SEQRES 14 A 499 PRO TYR TYR ALA GLY ASN LYS ASN ASP PHE ASP LYS LEU SEQRES 15 A 499 ILE PHE VAL PHE LEU ASP GLU ASP SER ALA PHE ALA ALA SEQRES 16 A 499 ALA GLN SER GLY GLN LEU GLY VAL VAL ARG ILE PRO PRO SEQRES 17 A 499 SER MET ALA VAL GLY SER VAL ASN ASN MET LYS LEU TRP SEQRES 18 A 499 VAL ARG PRO SER VAL GLU ASN ARG GLY ILE VAL PHE PRO SEQRES 19 A 499 THR THR PRO ALA GLY LYS LYS ASP ALA HIS GLY TYR PRO SEQRES 20 A 499 ILE GLY ASN ASP VAL THR ALA ASP VAL ALA ILE ARG ARG SEQRES 21 A 499 ALA ILE ASN TYR ALA ILE ASN ARG GLN LEU LEU ALA ASP SEQRES 22 A 499 GLN ILE MET GLU GLY HIS ALA ILE PRO ALA TYR THR GLY SEQRES 23 A 499 VAL GLN GLY LEU PRO TRP ASN ASN PRO ASP SER ALA ILE SEQRES 24 A 499 LYS ASP GLY ASP ILE ASP LYS ALA LYS GLN ILE LEU GLU SEQRES 25 A 499 GLN ALA GLY TRP GLN LEU ASN SER GLN GLY THR ARG GLU SEQRES 26 A 499 LYS ASN GLY LEU PRO ALA LYS ILE THR LEU TRP TYR THR SEQRES 27 A 499 SER GLY ASP THR THR ARG ARG ASP LEU ALA GLN ALA LEU SEQRES 28 A 499 ARG SER MET LEU LYS PRO ILE GLY ILE ASP VAL ASP LEU SEQRES 29 A 499 LYS SER GLY SER TRP GLU THR VAL GLU ARG ASN MET HIS SEQRES 30 A 499 ALA ASN PRO THR LEU PHE GLY TRP GLY SER LEU ASP PRO SEQRES 31 A 499 MET GLU LEU TYR HIS HIS TYR SER SER ASN ALA ALA GLY SEQRES 32 A 499 VAL GLU TYR TYR ASN PRO GLY TYR TYR LYS ASN PRO MET SEQRES 33 A 499 VAL ASP LYS HIS LEU GLN GLN ALA LEU ASP ALA PRO THR SEQRES 34 A 499 TRP GLN GLN ALA VAL PRO PHE TRP GLN GLN VAL ASP TRP SEQRES 35 A 499 ASP GLY THR THR GLY ALA GLY ILE ARG GLY ASP ALA ALA SEQRES 36 A 499 TRP ALA TRP LEU LEU ASN ILE GLN HIS THR TYR LEU ALA SEQRES 37 A 499 ASN ASN CYS VAL ASP LEU GLY LYS GLY THR PRO GLU ILE SEQRES 38 A 499 HIS GLY SER TRP SER LEU LEU ASN SER ILE ASP SER TRP SEQRES 39 A 499 LYS TRP THR CYS GLN SEQRES 1 B 499 ALA THR HIS THR LEU GLN LEU ALA ILE GLY ASP GLU PRO SEQRES 2 B 499 THR GLU GLY PHE ASP PRO MET LEU GLY TRP SER HIS GLY SEQRES 3 B 499 SER TYR LEU LEU LEU HIS SER PRO LEU LEU LYS GLN ASN SEQRES 4 B 499 GLU ASP PHE SER TRP ASP SER LEU LEU LEU SER GLN TYR SEQRES 5 B 499 GLN PRO SER ASP ASP GLY LYS THR TRP LEU LEU THR LEU SEQRES 6 B 499 LYS PRO ASP LEU LYS PHE SER ASP GLY SER PRO LEU THR SEQRES 7 B 499 ALA LYS ASP VAL ALA PHE THR TYR ASN ASN ALA ALA ALA SEQRES 8 B 499 SER GLY GLY LYS VAL ASP MET GLY ASN PHE LEU SER ALA SEQRES 9 B 499 GLU VAL ILE ASP PRO LEU ASN VAL ARG ILE HIS LEU LYS SEQRES 10 B 499 ALA PRO GLN SER THR PHE VAL ASN VAL LEU GLY SER LEU SEQRES 11 B 499 GLY ILE VAL SER ALA ASP LYS TYR ASN ALA LYS THR TYR SEQRES 12 B 499 ALA GLN LYS PRO ILE GLY ALA GLY PRO TYR ARG LEU VAL SEQRES 13 B 499 SER PHE GLN PRO GLY GLN GLN MET ILE VAL GLU ALA ASN SEQRES 14 B 499 PRO TYR TYR ALA GLY ASN LYS ASN ASP PHE ASP LYS LEU SEQRES 15 B 499 ILE PHE VAL PHE LEU ASP GLU ASP SER ALA PHE ALA ALA SEQRES 16 B 499 ALA GLN SER GLY GLN LEU GLY VAL VAL ARG ILE PRO PRO SEQRES 17 B 499 SER MET ALA VAL GLY SER VAL ASN ASN MET LYS LEU TRP SEQRES 18 B 499 VAL ARG PRO SER VAL GLU ASN ARG GLY ILE VAL PHE PRO SEQRES 19 B 499 THR THR PRO ALA GLY LYS LYS ASP ALA HIS GLY TYR PRO SEQRES 20 B 499 ILE GLY ASN ASP VAL THR ALA ASP VAL ALA ILE ARG ARG SEQRES 21 B 499 ALA ILE ASN TYR ALA ILE ASN ARG GLN LEU LEU ALA ASP SEQRES 22 B 499 GLN ILE MET GLU GLY HIS ALA ILE PRO ALA TYR THR GLY SEQRES 23 B 499 VAL GLN GLY LEU PRO TRP ASN ASN PRO ASP SER ALA ILE SEQRES 24 B 499 LYS ASP GLY ASP ILE ASP LYS ALA LYS GLN ILE LEU GLU SEQRES 25 B 499 GLN ALA GLY TRP GLN LEU ASN SER GLN GLY THR ARG GLU SEQRES 26 B 499 LYS ASN GLY LEU PRO ALA LYS ILE THR LEU TRP TYR THR SEQRES 27 B 499 SER GLY ASP THR THR ARG ARG ASP LEU ALA GLN ALA LEU SEQRES 28 B 499 ARG SER MET LEU LYS PRO ILE GLY ILE ASP VAL ASP LEU SEQRES 29 B 499 LYS SER GLY SER TRP GLU THR VAL GLU ARG ASN MET HIS SEQRES 30 B 499 ALA ASN PRO THR LEU PHE GLY TRP GLY SER LEU ASP PRO SEQRES 31 B 499 MET GLU LEU TYR HIS HIS TYR SER SER ASN ALA ALA GLY SEQRES 32 B 499 VAL GLU TYR TYR ASN PRO GLY TYR TYR LYS ASN PRO MET SEQRES 33 B 499 VAL ASP LYS HIS LEU GLN GLN ALA LEU ASP ALA PRO THR SEQRES 34 B 499 TRP GLN GLN ALA VAL PRO PHE TRP GLN GLN VAL ASP TRP SEQRES 35 B 499 ASP GLY THR THR GLY ALA GLY ILE ARG GLY ASP ALA ALA SEQRES 36 B 499 TRP ALA TRP LEU LEU ASN ILE GLN HIS THR TYR LEU ALA SEQRES 37 B 499 ASN ASN CYS VAL ASP LEU GLY LYS GLY THR PRO GLU ILE SEQRES 38 B 499 HIS GLY SER TRP SER LEU LEU ASN SER ILE ASP SER TRP SEQRES 39 B 499 LYS TRP THR CYS GLN HET NI A 501 1 HET HIS A 502 11 HET HIS A 503 11 HET NI B 501 1 HET HIS B 502 11 HET HIS B 503 11 HETNAM NI NICKEL (II) ION HETNAM HIS HISTIDINE FORMUL 3 NI 2(NI 2+) FORMUL 4 HIS 4(C6 H10 N3 O2 1+) FORMUL 9 HOH *106(H2 O) HELIX 1 1 SER A 27 HIS A 32 1 6 HELIX 2 2 THR A 78 GLY A 93 1 16 HELIX 3 3 THR A 122 GLY A 128 1 7 HELIX 4 4 ASN A 139 ALA A 144 1 6 HELIX 5 5 ASP A 188 SER A 198 1 11 HELIX 6 6 PRO A 207 ALA A 211 5 5 HELIX 7 7 ASP A 255 ILE A 266 1 12 HELIX 8 8 ASN A 267 MET A 276 1 10 HELIX 9 9 ASP A 303 ALA A 314 1 12 HELIX 10 10 ASP A 341 LYS A 356 1 16 HELIX 11 11 PRO A 357 GLY A 359 5 3 HELIX 12 12 SER A 368 MET A 376 1 9 HELIX 13 13 PRO A 390 SER A 398 1 9 HELIX 14 14 SER A 399 ALA A 402 5 4 HELIX 15 15 ASN A 414 ASP A 426 1 13 HELIX 16 16 THR A 429 VAL A 440 1 12 HELIX 17 17 TRP A 485 TRP A 494 5 10 HELIX 18 18 SER B 27 HIS B 32 1 6 HELIX 19 19 THR B 78 SER B 92 1 15 HELIX 20 20 THR B 122 GLY B 128 1 7 HELIX 21 21 ASP B 188 SER B 198 1 11 HELIX 22 22 PRO B 207 ALA B 211 5 5 HELIX 23 23 ASP B 255 ILE B 266 1 12 HELIX 24 24 ASN B 267 MET B 276 1 10 HELIX 25 25 ASP B 303 ALA B 314 1 12 HELIX 26 26 ASP B 341 LEU B 355 1 15 HELIX 27 27 LYS B 356 GLY B 359 5 4 HELIX 28 28 SER B 368 MET B 376 1 9 HELIX 29 29 PRO B 390 SER B 398 1 9 HELIX 30 30 SER B 399 ALA B 402 5 4 HELIX 31 31 ASN B 414 ASP B 426 1 13 HELIX 32 32 THR B 429 VAL B 440 1 12 HELIX 33 33 TRP B 485 TRP B 494 5 10 SHEET 1 A 7 TYR A 153 GLN A 159 0 SHEET 2 A 7 GLN A 163 ALA A 168 -1 O GLU A 167 N ARG A 154 SHEET 3 A 7 LYS A 181 VAL A 185 -1 O PHE A 184 N MET A 164 SHEET 4 A 7 THR A 4 ALA A 8 1 N LEU A 5 O ILE A 183 SHEET 5 A 7 VAL A 203 ILE A 206 1 O ARG A 205 N ALA A 8 SHEET 6 A 7 HIS A 464 ASN A 469 -1 O LEU A 467 N VAL A 204 SHEET 7 A 7 MET A 218 ARG A 223 -1 N ARG A 223 O HIS A 464 SHEET 1 B 2 LEU A 36 GLN A 38 0 SHEET 2 B 2 TRP A 44 SER A 46 -1 O ASP A 45 N LYS A 37 SHEET 1 C 4 LEU A 49 PRO A 54 0 SHEET 2 C 4 THR A 60 LEU A 65 -1 O THR A 64 N GLN A 51 SHEET 3 C 4 ASN A 111 LEU A 116 -1 O VAL A 112 N LEU A 63 SHEET 4 C 4 PHE A 101 ASP A 108 -1 N LEU A 102 O HIS A 115 SHEET 1 D 2 LEU A 69 LYS A 70 0 SHEET 2 D 2 PRO A 76 LEU A 77 -1 O LEU A 77 N LEU A 69 SHEET 1 E 4 ALA A 280 PRO A 282 0 SHEET 2 E 4 TRP A 456 ILE A 462 -1 O ASN A 461 N ILE A 281 SHEET 3 E 4 ASN A 228 VAL A 232 -1 N ILE A 231 O ALA A 457 SHEET 4 E 4 THR A 381 PHE A 383 -1 O PHE A 383 N GLY A 230 SHEET 1 F 2 LYS A 240 LYS A 241 0 SHEET 2 F 2 PRO A 247 ILE A 248 -1 O ILE A 248 N LYS A 240 SHEET 1 G 3 GLN A 317 LEU A 318 0 SHEET 2 G 3 ARG A 324 LYS A 326 -1 O GLU A 325 N GLN A 317 SHEET 3 G 3 LEU A 329 PRO A 330 -1 O LEU A 329 N LYS A 326 SHEET 1 H 2 LYS A 332 THR A 338 0 SHEET 2 H 2 ASP A 361 GLY A 367 1 O ASP A 363 N ILE A 333 SHEET 1 I 2 VAL A 472 ASP A 473 0 SHEET 2 I 2 LYS A 495 TRP A 496 -1 O LYS A 495 N ASP A 473 SHEET 1 J 7 TYR B 153 GLN B 159 0 SHEET 2 J 7 GLN B 163 ALA B 168 -1 O ILE B 165 N VAL B 156 SHEET 3 J 7 LYS B 181 VAL B 185 -1 O PHE B 184 N MET B 164 SHEET 4 J 7 THR B 4 ALA B 8 1 N LEU B 5 O ILE B 183 SHEET 5 J 7 VAL B 203 ILE B 206 1 O ARG B 205 N ALA B 8 SHEET 6 J 7 HIS B 464 ASN B 469 -1 O THR B 465 N ILE B 206 SHEET 7 J 7 MET B 218 ARG B 223 -1 N ARG B 223 O HIS B 464 SHEET 1 K 2 LEU B 36 GLN B 38 0 SHEET 2 K 2 TRP B 44 SER B 46 -1 O ASP B 45 N LYS B 37 SHEET 1 L 4 LEU B 49 PRO B 54 0 SHEET 2 L 4 THR B 60 LEU B 65 -1 O THR B 64 N GLN B 51 SHEET 3 L 4 ASN B 111 LEU B 116 -1 O VAL B 112 N LEU B 63 SHEET 4 L 4 PHE B 101 ASP B 108 -1 N GLU B 105 O ARG B 113 SHEET 1 M 2 LEU B 69 LYS B 70 0 SHEET 2 M 2 PRO B 76 LEU B 77 -1 O LEU B 77 N LEU B 69 SHEET 1 N 4 ALA B 280 PRO B 282 0 SHEET 2 N 4 TRP B 456 ILE B 462 -1 O ASN B 461 N ILE B 281 SHEET 3 N 4 ASN B 228 VAL B 232 -1 N ILE B 231 O ALA B 457 SHEET 4 N 4 THR B 381 TRP B 385 -1 O TRP B 385 N ASN B 228 SHEET 1 O 2 LYS B 240 LYS B 241 0 SHEET 2 O 2 PRO B 247 ILE B 248 -1 O ILE B 248 N LYS B 240 SHEET 1 P 3 GLN B 317 LEU B 318 0 SHEET 2 P 3 ARG B 324 LYS B 326 -1 O GLU B 325 N GLN B 317 SHEET 3 P 3 LEU B 329 PRO B 330 -1 O LEU B 329 N LYS B 326 SHEET 1 Q 2 LYS B 332 THR B 338 0 SHEET 2 Q 2 ASP B 361 GLY B 367 1 O ASP B 363 N LEU B 335 SHEET 1 R 2 VAL B 472 ASP B 473 0 SHEET 2 R 2 LYS B 495 TRP B 496 -1 O LYS B 495 N ASP B 473 SSBOND 1 CYS A 471 CYS A 498 1555 1555 2.03 SSBOND 2 CYS B 471 CYS B 498 1555 1555 2.03 LINK NE2 HIS A 482 NI NI A 501 1555 1555 2.23 LINK NI NI A 501 N HIS A 502 1555 1555 1.97 LINK NI NI A 501 ND1 HIS A 502 1555 1555 2.19 LINK NI NI A 501 OXT HIS A 502 1555 1555 2.25 LINK NI NI A 501 O HIS A 503 1555 1555 1.81 LINK NI NI A 501 ND1 HIS A 503 1555 1555 1.82 LINK NE2 HIS B 482 NI NI B 501 1555 1555 2.47 LINK NI NI B 501 N HIS B 502 1555 1555 1.90 LINK NI NI B 501 OXT HIS B 502 1555 1555 2.09 LINK NI NI B 501 ND1 HIS B 502 1555 1555 2.26 LINK NI NI B 501 ND1 HIS B 503 1555 1555 2.01 LINK NI NI B 501 O HIS B 503 1555 1555 2.07 SITE 1 AC1 3 HIS A 482 HIS A 502 HIS A 503 SITE 1 AC2 10 ARG A 344 TRP A 369 PHE A 383 GLY A 384 SITE 2 AC2 10 TRP A 385 TYR A 406 HIS A 482 NI A 501 SITE 3 AC2 10 HIS A 503 HOH A 611 SITE 1 AC3 4 HIS A 482 NI A 501 HIS A 502 HOH A 661 SITE 1 AC4 3 HIS B 482 HIS B 502 HIS B 503 SITE 1 AC5 9 ARG B 344 TRP B 369 PHE B 383 GLY B 384 SITE 2 AC5 9 TRP B 385 TYR B 406 HIS B 482 NI B 501 SITE 3 AC5 9 HIS B 503 SITE 1 AC6 5 ARG B 344 HIS B 482 GLY B 483 NI B 501 SITE 2 AC6 5 HIS B 502 CRYST1 47.040 213.830 52.870 90.00 102.72 90.00 P 1 21 1 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 0.021259 0.000000 0.004799 0.00000 SCALE2 0.000000 0.004677 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019390 0.00000