HEADER METAL TRANSPORT 22-JUL-03 1UIV TITLE CRYSTAL STRUCTURES OF THE LIGANDED AND UNLIGANDED NICKEL BINDING TITLE 2 PROTEIN NIKA FROM ESCHERICHIA COLI (NICKEL LIGANDED FORM) CAVEAT 1UIV ASP A 4 HAS WRONG CHIRALITY AT ATOM CA COMPND MOL_ID: 1; COMPND 2 MOLECULE: NICKEL-BINDING PERIPLASMIC PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NIKA, NICKEL BINDING PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: NIKA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS NICKEL BINDING PROTEIN, NICKEL LIGANDED FORM, METAL TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR J.HEDDLE,D.J.SCOTT,S.UNZAI,S.-Y.PARK,J.R.H.TAME REVDAT 5 27-DEC-23 1UIV 1 REMARK REVDAT 4 10-NOV-21 1UIV 1 SEQADV REVDAT 3 19-AUG-20 1UIV 1 CAVEAT REMARK LINK REVDAT 2 24-FEB-09 1UIV 1 VERSN REVDAT 1 03-FEB-04 1UIV 0 JRNL AUTH J.HEDDLE,D.J.SCOTT,S.UNZAI,S.-Y.PARK,J.R.H.TAME JRNL TITL CRYSTAL STRUCTURES OF THE LIGANDED AND UNLIGANDED JRNL TITL 2 NICKEL-BINDING PROTEIN NIKA FROM ESCHERICHIA COLI JRNL REF J.BIOL.CHEM. V. 278 50322 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12960164 JRNL DOI 10.1074/JBC.M307941200 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.19 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 66817 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3588 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3569 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1940 REMARK 3 BIN FREE R VALUE SET COUNT : 185 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7889 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 491 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.31000 REMARK 3 B22 (A**2) : -0.73000 REMARK 3 B33 (A**2) : 1.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.199 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.179 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.125 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.320 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8096 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11026 ; 2.090 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 991 ; 7.567 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1207 ; 0.202 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6250 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3917 ; 0.236 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 485 ; 0.169 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 84 ; 0.257 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.371 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4986 ; 1.113 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 8075 ; 1.916 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3110 ; 3.318 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2951 ; 5.098 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UIV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1000005871. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66817 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.11400 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG2000, AMMONIUM SULFATE, PH 8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 34.86000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 96.40300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.86000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 96.40300 REMARK 290 SMTRY3 4 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 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 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 ALA A 2 REMARK 465 PRO A 3 REMARK 465 LYS A 501 REMARK 465 PRO A 502 REMARK 465 ALA B 1001 REMARK 465 ALA B 1002 REMARK 465 PRO B 1003 REMARK 465 VAL B 1500 REMARK 465 LYS B 1501 REMARK 465 PRO B 1502 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 GLN A 174 CB GLN A 174 CG 0.206 REMARK 500 GLU A 479 CD GLU A 479 OE2 0.084 REMARK 500 GLU B1444 CD GLU B1444 OE1 0.105 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 ASP A 4 CB - CA - C ANGL. DEV. = 38.2 DEGREES REMARK 500 VAL A 12 CG1 - CB - CG2 ANGL. DEV. = 11.9 DEGREES REMARK 500 ASP A 43 CB - CG - OD2 ANGL. DEV. = 7.9 DEGREES REMARK 500 ASP A 70 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 137 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 137 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 GLY A 329 N - CA - C ANGL. DEV. = -17.7 DEGREES REMARK 500 LEU A 352 CA - CB - CG ANGL. DEV. = 22.7 DEGREES REMARK 500 ARG A 396 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 SER A 415 C - N - CA ANGL. DEV. = -16.0 DEGREES REMARK 500 ASP A 427 CB - CG - OD1 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 427 CB - CG - OD2 ANGL. DEV. = 9.0 DEGREES REMARK 500 VAL A 438 CB - CA - C ANGL. DEV. = -13.2 DEGREES REMARK 500 ARG A 452 CG - CD - NE ANGL. DEV. = -15.3 DEGREES REMARK 500 ARG A 452 CD - NE - CZ ANGL. DEV. = 8.9 DEGREES REMARK 500 ARG A 452 NE - CZ - NH1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG A 452 NE - CZ - NH2 ANGL. DEV. = -12.4 DEGREES REMARK 500 ASP A 453 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 457 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP B1004 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 VAL B1038 CG1 - CB - CG2 ANGL. DEV. = 10.8 DEGREES REMARK 500 HIS B1056 N - CA - CB ANGL. DEV. = -11.4 DEGREES REMARK 500 ASP B1080 CB - CG - OD2 ANGL. DEV. = 7.3 DEGREES REMARK 500 ASP B1109 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG B1137 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ASP B1201 CB - CG - OD2 ANGL. DEV. = 8.4 DEGREES REMARK 500 LEU B1216 CA - CB - CG ANGL. DEV. = 17.2 DEGREES REMARK 500 LEU B1223 CA - CB - CG ANGL. DEV. = 14.3 DEGREES REMARK 500 ASP B1280 CB - CG - OD2 ANGL. DEV. = 6.8 DEGREES REMARK 500 GLY B1304 C - N - CA ANGL. DEV. = -25.6 DEGREES REMARK 500 ARG B1333 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG B1333 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ASP B1350 CB - CG - OD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 ILE B1367 CG1 - CB - CG2 ANGL. DEV. = 18.2 DEGREES REMARK 500 ASP B1427 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP B1443 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG B1447 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG B1447 NE - CZ - NH2 ANGL. DEV. = -6.1 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 TYR A 22 -137.22 -110.39 REMARK 500 TRP A 49 -104.65 -136.91 REMARK 500 PHE A 139 52.69 -91.62 REMARK 500 LYS A 148 -65.16 -94.98 REMARK 500 LYS A 157 -96.07 -81.40 REMARK 500 ASP A 311 84.33 -154.77 REMARK 500 THR B1008 -167.95 -128.22 REMARK 500 TYR B1022 -136.39 -114.81 REMARK 500 TRP B1049 -112.81 -142.78 REMARK 500 SER B1114 -163.90 -169.69 REMARK 500 LYS B1157 -92.38 -83.41 REMARK 500 GLN B1174 -69.75 -121.73 REMARK 500 ASN B1220 6.08 -159.90 REMARK 500 GLU B1221 51.14 -112.60 REMARK 500 ASN B1281 -78.81 -91.68 REMARK 500 ASP B1311 85.57 -159.18 REMARK 500 PRO B1327 150.01 -47.75 REMARK 500 GLU B1378 -59.14 -23.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 328 GLY A 329 -51.25 REMARK 500 THR B 1055 HIS B 1056 -135.99 REMARK 500 GLY B 1304 LEU B 1305 -146.39 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 503 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 644 O REMARK 620 2 HOH A 710 O 71.4 REMARK 620 3 HOH A 711 O 80.6 148.1 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 1503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UIU RELATED DB: PDB REMARK 900 NICKEL UNLIGANDED FORM DBREF 1UIV A 1 502 UNP P33590 NIKA_ECOLI 23 524 DBREF 1UIV B 1001 1502 UNP P33590 NIKA_ECOLI 23 524 SEQADV 1UIV ARG A 361 UNP P33590 GLN 383 ENGINEERED MUTATION SEQADV 1UIV ARG B 1361 UNP P33590 GLN 383 ENGINEERED MUTATION SEQRES 1 A 502 ALA ALA PRO ASP GLU ILE THR THR ALA TRP PRO VAL ASN SEQRES 2 A 502 VAL GLY PRO LEU ASN PRO HIS LEU TYR THR PRO ASN GLN SEQRES 3 A 502 MET PHE ALA GLN SER MET VAL TYR GLU PRO LEU VAL LYS SEQRES 4 A 502 TYR GLN ALA ASP GLY SER VAL ILE PRO TRP LEU ALA LYS SEQRES 5 A 502 SER TRP THR HIS SER GLU ASP GLY LYS THR TRP THR PHE SEQRES 6 A 502 THR LEU ARG ASP ASP VAL LYS PHE SER ASN GLY GLU PRO SEQRES 7 A 502 PHE ASP ALA GLU ALA ALA ALA GLU ASN PHE ARG ALA VAL SEQRES 8 A 502 LEU ASP ASN ARG GLN ARG HIS ALA TRP LEU GLU LEU ALA SEQRES 9 A 502 ASN GLN ILE VAL ASP VAL LYS ALA LEU SER LYS THR GLU SEQRES 10 A 502 LEU GLN ILE THR LEU LYS SER ALA TYR TYR PRO PHE LEU SEQRES 11 A 502 GLN GLU LEU ALA LEU PRO ARG PRO PHE ARG PHE ILE ALA SEQRES 12 A 502 PRO SER GLN PHE LYS ASN HIS GLU THR MET ASN GLY ILE SEQRES 13 A 502 LYS ALA PRO ILE GLY THR GLY PRO TRP ILE LEU GLN GLU SEQRES 14 A 502 SER LYS LEU ASN GLN TYR ASP VAL PHE VAL ARG ASN GLU SEQRES 15 A 502 ASN TYR TRP GLY GLU LYS PRO ALA ILE LYS LYS ILE THR SEQRES 16 A 502 PHE ASN VAL ILE PRO ASP PRO THR THR ARG ALA VAL ALA SEQRES 17 A 502 PHE GLU THR GLY ASP ILE ASP LEU LEU TYR GLY ASN GLU SEQRES 18 A 502 GLY LEU LEU PRO LEU ASP THR PHE ALA ARG PHE SER GLN SEQRES 19 A 502 ASN PRO ALA TYR HIS THR GLN LEU SER GLN PRO ILE GLU SEQRES 20 A 502 THR VAL MET LEU ALA LEU ASN THR ALA LYS ALA PRO THR SEQRES 21 A 502 ASN GLU LEU ALA VAL ARG GLU ALA LEU ASN TYR ALA VAL SEQRES 22 A 502 ASN LYS LYS SER LEU ILE ASP ASN ALA LEU TYR GLY THR SEQRES 23 A 502 GLN GLN VAL ALA ASP THR LEU PHE ALA PRO SER VAL PRO SEQRES 24 A 502 TYR ALA ASN LEU GLY LEU LYS PRO SER GLN TYR ASP PRO SEQRES 25 A 502 GLN LYS ALA LYS ALA LEU LEU GLU LYS ALA GLY TRP THR SEQRES 26 A 502 LEU PRO ALA GLY LYS ASP ILE ARG GLU LYS ASN GLY GLN SEQRES 27 A 502 PRO LEU ARG ILE GLU LEU SER PHE ILE GLY THR ASP ALA SEQRES 28 A 502 LEU SER LYS SER MET ALA GLU ILE ILE ARG ALA ASP MET SEQRES 29 A 502 ARG GLN ILE GLY ALA ASP VAL SER LEU ILE GLY GLU GLU SEQRES 30 A 502 GLU SER SER ILE TYR ALA ARG GLN ARG ASP GLY ARG PHE SEQRES 31 A 502 GLY MET ILE PHE HIS ARG THR TRP GLY ALA PRO TYR ASP SEQRES 32 A 502 PRO HIS ALA PHE LEU SER SER MET ARG VAL PRO SER HIS SEQRES 33 A 502 ALA ASP PHE GLN ALA GLN GLN GLY LEU ALA ASP LYS PRO SEQRES 34 A 502 LEU ILE ASP LYS GLU ILE GLY GLU VAL LEU ALA THR HIS SEQRES 35 A 502 ASP GLU THR GLN ARG GLN ALA LEU TYR ARG ASP ILE LEU SEQRES 36 A 502 THR ARG LEU HIS ASP GLU ALA VAL TYR LEU PRO ILE SER SEQRES 37 A 502 TYR ILE SER MET MET VAL VAL SER LYS PRO GLU LEU GLY SEQRES 38 A 502 ASN ILE PRO TYR ALA PRO ILE ALA THR GLU ILE PRO PHE SEQRES 39 A 502 GLU GLN ILE LYS PRO VAL LYS PRO SEQRES 1 B 502 ALA ALA PRO ASP GLU ILE THR THR ALA TRP PRO VAL ASN SEQRES 2 B 502 VAL GLY PRO LEU ASN PRO HIS LEU TYR THR PRO ASN GLN SEQRES 3 B 502 MET PHE ALA GLN SER MET VAL TYR GLU PRO LEU VAL LYS SEQRES 4 B 502 TYR GLN ALA ASP GLY SER VAL ILE PRO TRP LEU ALA LYS SEQRES 5 B 502 SER TRP THR HIS SER GLU ASP GLY LYS THR TRP THR PHE SEQRES 6 B 502 THR LEU ARG ASP ASP VAL LYS PHE SER ASN GLY GLU PRO SEQRES 7 B 502 PHE ASP ALA GLU ALA ALA ALA GLU ASN PHE ARG ALA VAL SEQRES 8 B 502 LEU ASP ASN ARG GLN ARG HIS ALA TRP LEU GLU LEU ALA SEQRES 9 B 502 ASN GLN ILE VAL ASP VAL LYS ALA LEU SER LYS THR GLU SEQRES 10 B 502 LEU GLN ILE THR LEU LYS SER ALA TYR TYR PRO PHE LEU SEQRES 11 B 502 GLN GLU LEU ALA LEU PRO ARG PRO PHE ARG PHE ILE ALA SEQRES 12 B 502 PRO SER GLN PHE LYS ASN HIS GLU THR MET ASN GLY ILE SEQRES 13 B 502 LYS ALA PRO ILE GLY THR GLY PRO TRP ILE LEU GLN GLU SEQRES 14 B 502 SER LYS LEU ASN GLN TYR ASP VAL PHE VAL ARG ASN GLU SEQRES 15 B 502 ASN TYR TRP GLY GLU LYS PRO ALA ILE LYS LYS ILE THR SEQRES 16 B 502 PHE ASN VAL ILE PRO ASP PRO THR THR ARG ALA VAL ALA SEQRES 17 B 502 PHE GLU THR GLY ASP ILE ASP LEU LEU TYR GLY ASN GLU SEQRES 18 B 502 GLY LEU LEU PRO LEU ASP THR PHE ALA ARG PHE SER GLN SEQRES 19 B 502 ASN PRO ALA TYR HIS THR GLN LEU SER GLN PRO ILE GLU SEQRES 20 B 502 THR VAL MET LEU ALA LEU ASN THR ALA LYS ALA PRO THR SEQRES 21 B 502 ASN GLU LEU ALA VAL ARG GLU ALA LEU ASN TYR ALA VAL SEQRES 22 B 502 ASN LYS LYS SER LEU ILE ASP ASN ALA LEU TYR GLY THR SEQRES 23 B 502 GLN GLN VAL ALA ASP THR LEU PHE ALA PRO SER VAL PRO SEQRES 24 B 502 TYR ALA ASN LEU GLY LEU LYS PRO SER GLN TYR ASP PRO SEQRES 25 B 502 GLN LYS ALA LYS ALA LEU LEU GLU LYS ALA GLY TRP THR SEQRES 26 B 502 LEU PRO ALA GLY LYS ASP ILE ARG GLU LYS ASN GLY GLN SEQRES 27 B 502 PRO LEU ARG ILE GLU LEU SER PHE ILE GLY THR ASP ALA SEQRES 28 B 502 LEU SER LYS SER MET ALA GLU ILE ILE ARG ALA ASP MET SEQRES 29 B 502 ARG GLN ILE GLY ALA ASP VAL SER LEU ILE GLY GLU GLU SEQRES 30 B 502 GLU SER SER ILE TYR ALA ARG GLN ARG ASP GLY ARG PHE SEQRES 31 B 502 GLY MET ILE PHE HIS ARG THR TRP GLY ALA PRO TYR ASP SEQRES 32 B 502 PRO HIS ALA PHE LEU SER SER MET ARG VAL PRO SER HIS SEQRES 33 B 502 ALA ASP PHE GLN ALA GLN GLN GLY LEU ALA ASP LYS PRO SEQRES 34 B 502 LEU ILE ASP LYS GLU ILE GLY GLU VAL LEU ALA THR HIS SEQRES 35 B 502 ASP GLU THR GLN ARG GLN ALA LEU TYR ARG ASP ILE LEU SEQRES 36 B 502 THR ARG LEU HIS ASP GLU ALA VAL TYR LEU PRO ILE SER SEQRES 37 B 502 TYR ILE SER MET MET VAL VAL SER LYS PRO GLU LEU GLY SEQRES 38 B 502 ASN ILE PRO TYR ALA PRO ILE ALA THR GLU ILE PRO PHE SEQRES 39 B 502 GLU GLN ILE LYS PRO VAL LYS PRO HET NI A 503 1 HET NI B1503 1 HETNAM NI NICKEL (II) ION FORMUL 3 NI 2(NI 2+) FORMUL 5 HOH *491(H2 O) HELIX 1 1 GLN A 26 TYR A 34 1 9 HELIX 2 2 ASP A 80 ASP A 93 1 14 HELIX 3 3 ASN A 94 ALA A 99 5 6 HELIX 4 4 LEU A 101 GLN A 106 1 6 HELIX 5 5 PRO A 128 ALA A 134 1 7 HELIX 6 6 ALA A 143 PHE A 147 5 5 HELIX 7 7 ASP A 201 THR A 211 1 11 HELIX 8 8 PRO A 225 GLN A 234 1 10 HELIX 9 9 GLU A 262 VAL A 273 1 12 HELIX 10 10 ASN A 274 LEU A 283 1 10 HELIX 11 11 ASP A 311 ALA A 322 1 12 HELIX 12 12 ASP A 350 GLN A 366 1 17 HELIX 13 13 GLU A 377 GLY A 388 1 12 HELIX 14 14 PRO A 404 MET A 411 1 8 HELIX 15 15 HIS A 416 GLN A 422 1 7 HELIX 16 16 ASP A 427 ALA A 440 1 14 HELIX 17 17 ASP A 443 GLU A 461 1 19 HELIX 18 18 PRO A 478 GLY A 481 5 4 HELIX 19 19 PRO A 493 ILE A 497 5 5 HELIX 20 20 GLN B 1026 TYR B 1034 1 9 HELIX 21 21 ASP B 1080 ASP B 1093 1 14 HELIX 22 22 ASN B 1094 ALA B 1099 5 6 HELIX 23 23 LEU B 1101 GLN B 1106 1 6 HELIX 24 24 PRO B 1128 ALA B 1134 1 7 HELIX 25 25 ALA B 1143 SER B 1145 5 3 HELIX 26 26 ASP B 1201 THR B 1211 1 11 HELIX 27 27 PRO B 1225 GLN B 1234 1 10 HELIX 28 28 GLU B 1262 VAL B 1273 1 12 HELIX 29 29 ASN B 1274 ASN B 1281 1 8 HELIX 30 30 ASP B 1311 ALA B 1322 1 12 HELIX 31 31 ASP B 1350 GLN B 1366 1 17 HELIX 32 32 GLU B 1377 GLY B 1388 1 12 HELIX 33 33 PRO B 1404 MET B 1411 1 8 HELIX 34 34 HIS B 1416 GLN B 1423 1 8 HELIX 35 35 ASP B 1427 THR B 1441 1 15 HELIX 36 36 ASP B 1443 GLU B 1461 1 19 HELIX 37 37 PRO B 1478 GLY B 1481 5 4 HELIX 38 38 PRO B 1493 ILE B 1497 5 5 SHEET 1 A 4 GLU A 5 TRP A 10 0 SHEET 2 A 4 LYS A 193 VAL A 198 1 O THR A 195 N THR A 8 SHEET 3 A 4 TYR A 175 ARG A 180 -1 N PHE A 178 O ILE A 194 SHEET 4 A 4 TRP A 165 LEU A 167 -1 N ILE A 166 O VAL A 179 SHEET 1 B 2 VAL A 38 TYR A 40 0 SHEET 2 B 2 VAL A 46 PRO A 48 -1 O ILE A 47 N LYS A 39 SHEET 1 C 4 ALA A 51 HIS A 56 0 SHEET 2 C 4 THR A 62 LEU A 67 -1 O THR A 66 N SER A 53 SHEET 3 C 4 GLU A 117 LEU A 122 -1 O LEU A 118 N PHE A 65 SHEET 4 C 4 ILE A 107 SER A 114 -1 N LYS A 111 O GLN A 119 SHEET 1 D 3 LEU A 216 TYR A 218 0 SHEET 2 D 3 TYR A 464 SER A 476 -1 O VAL A 475 N LEU A 217 SHEET 3 D 3 GLN A 288 VAL A 289 -1 N GLN A 288 O TYR A 469 SHEET 1 E 6 LEU A 216 TYR A 218 0 SHEET 2 E 6 TYR A 464 SER A 476 -1 O VAL A 475 N LEU A 217 SHEET 3 E 6 HIS A 239 LEU A 253 -1 N VAL A 249 O SER A 468 SHEET 4 E 6 MET A 392 ARG A 396 -1 O ILE A 393 N ALA A 252 SHEET 5 E 6 ARG A 341 ILE A 347 1 N SER A 345 O MET A 392 SHEET 6 E 6 ASP A 370 GLU A 376 1 O SER A 372 N LEU A 344 SHEET 1 F 2 GLU A 334 LYS A 335 0 SHEET 2 F 2 GLN A 338 PRO A 339 -1 O GLN A 338 N LYS A 335 SHEET 1 G 4 GLU B1005 TRP B1010 0 SHEET 2 G 4 LYS B1193 VAL B1198 1 O THR B1195 N THR B1008 SHEET 3 G 4 TYR B1175 ARG B1180 -1 N ASP B1176 O PHE B1196 SHEET 4 G 4 TRP B1165 LYS B1171 -1 N LYS B1171 O TYR B1175 SHEET 1 H 2 VAL B1038 TYR B1040 0 SHEET 2 H 2 VAL B1046 PRO B1048 -1 O ILE B1047 N LYS B1039 SHEET 1 I 4 ALA B1051 HIS B1056 0 SHEET 2 I 4 THR B1062 LEU B1067 -1 O THR B1066 N SER B1053 SHEET 3 I 4 GLU B1117 LEU B1122 -1 O LEU B1118 N PHE B1065 SHEET 4 I 4 ILE B1107 ALA B1112 -1 N LYS B1111 O GLN B1119 SHEET 1 J 2 PHE B1147 LYS B1148 0 SHEET 2 J 2 GLU B1151 ILE B1156 -1 O GLU B1151 N LYS B1148 SHEET 1 K 3 LEU B1216 GLY B1219 0 SHEET 2 K 3 MET B1473 SER B1476 -1 O MET B1473 N GLY B1219 SHEET 3 K 3 HIS B1239 LEU B1242 -1 N HIS B1239 O SER B1476 SHEET 1 L 6 GLN B1288 VAL B1289 0 SHEET 2 L 6 TYR B1464 ILE B1470 -1 O TYR B1469 N GLN B1288 SHEET 3 L 6 GLU B1247 LEU B1253 -1 N VAL B1249 O SER B1468 SHEET 4 L 6 MET B1392 ARG B1396 -1 O HIS B1395 N MET B1250 SHEET 5 L 6 ARG B1341 ILE B1347 1 N SER B1345 O MET B1392 SHEET 6 L 6 ASP B1370 GLU B1376 1 O GLU B1376 N PHE B1346 SHEET 1 M 2 GLU B1334 LYS B1335 0 SHEET 2 M 2 GLN B1338 PRO B1339 -1 O GLN B1338 N LYS B1335 LINK NI NI A 503 O HOH A 644 1555 1555 2.71 LINK NI NI A 503 O HOH A 710 1555 1555 2.45 LINK NI NI A 503 O HOH A 711 1555 1555 2.66 LINK O HOH B 441 NI NI B1503 1555 1555 2.38 CISPEP 1 THR A 23 PRO A 24 0 9.60 CISPEP 2 ARG A 137 PRO A 138 0 5.98 CISPEP 3 ALA A 258 PRO A 259 0 -7.22 CISPEP 4 ALA A 400 PRO A 401 0 -4.17 CISPEP 5 ASP A 403 PRO A 404 0 1.55 CISPEP 6 THR B 1023 PRO B 1024 0 12.89 CISPEP 7 ARG B 1137 PRO B 1138 0 8.41 CISPEP 8 ALA B 1258 PRO B 1259 0 -1.50 CISPEP 9 ALA B 1400 PRO B 1401 0 -0.72 CISPEP 10 ASP B 1403 PRO B 1404 0 -0.16 SITE 1 AC1 5 HOH A 621 HOH A 634 HOH A 644 HOH A 710 SITE 2 AC1 5 HOH A 711 SITE 1 AC2 3 HOH B 320 HOH B 433 HOH B 441 CRYST1 69.720 192.806 75.143 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 0.014343 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005187 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013308 0.00000