HEADER HYDROLASE 26-OCT-06 2NOO TITLE CRYSTAL STRUCTURE OF MUTANT NIKA COMPND MOL_ID: 1; COMPND 2 MOLECULE: NICKEL-BINDING PERIPLASMIC PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NIKA; COMPND 5 EC: 3.6.3.24; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: NIKA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS NICKEL-BOUND, TRANSPORT, IODINE, PERIPLASM, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.ADDY,M.OHARA,F.KAWAI,A.KIDERA,M.IKEGUCHI,S.FUCHIGAMI,M.OSAWA, AUTHOR 2 I.SHIMADA,S.Y.PARK,J.R.H.TAME,J.G.HEDDLE REVDAT 3 18-OCT-17 2NOO 1 REMARK REVDAT 2 24-FEB-09 2NOO 1 VERSN REVDAT 1 23-JAN-07 2NOO 0 JRNL AUTH C.ADDY,M.OHARA,F.KAWAI,A.KIDERA,M.IKEGUCHI,S.FUCHIGAMI, JRNL AUTH 2 M.OSAWA,I.SHIMADA,S.Y.PARK,J.R.TAME,J.G.HEDDLE JRNL TITL NICKEL BINDING TO NIKA: AN ADDITIONAL BINDING SITE JRNL TITL 2 RECONCILES SPECTROSCOPY, CALORIMETRY AND CRYSTALLOGRAPHY. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 63 221 2007 JRNL REFN ISSN 0907-4449 JRNL PMID 17242515 JRNL DOI 10.1107/S0907444906048712 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 54867 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2788 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2844 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2030 REMARK 3 BIN FREE R VALUE SET COUNT : 154 REMARK 3 BIN FREE R VALUE : 0.2490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3899 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 348 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : -0.01000 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): 0.104 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.101 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.062 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.776 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4002 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3588 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5446 ; 1.546 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8388 ; 0.802 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 495 ; 6.200 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 182 ;38.128 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 654 ;13.948 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;20.010 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 603 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4453 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 759 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 828 ; 0.232 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3635 ; 0.195 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1995 ; 0.182 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2127 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 261 ; 0.143 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.112 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 14 ; 0.140 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 49 ; 0.284 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 26 ; 0.138 ; 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): 2499 ; 0.900 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 983 ; 0.250 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4027 ; 1.559 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1649 ; 2.680 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1419 ; 4.081 ; 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2NOO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000040118. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JAN-06 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A 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 : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54989 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.20500 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: MOLREP REMARK 200 STARTING MODEL: 1UIV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, AMMONIUM SULFATE, SODIUM REMARK 280 IODIDE, NICKEL CHLORIDE, PH 5.5, HANGING DROP, TEMPERATURE 293K 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 21.73500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.19150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.12400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.19150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.73500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.12400 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 300 REMARK: THE ASYMETRIC UNIT CONTAINS ONE MONOMER. THE BIOLOGICAL REMARK 300 ASSEMBLY IS ONE MONOMER. 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 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 VAL A 500 REMARK 465 LYS A 501 REMARK 465 PRO A 502 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 OE1 GLN A 30 O HOH A 1429 2.10 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 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 95 NE - CZ - NH2 ANGL. DEV. = -4.7 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 TRP A 49 -107.53 -141.89 REMARK 500 PHE A 139 53.05 -92.37 REMARK 500 LYS A 157 -113.96 -88.73 REMARK 500 GLN A 174 -63.50 -128.55 REMARK 500 ASP A 213 59.97 -92.32 REMARK 500 ILE A 246 -82.98 -109.23 REMARK 500 ASN A 281 -70.03 -88.91 REMARK 500 TYI A 300 -2.31 77.27 REMARK 500 ASP A 311 84.54 -155.95 REMARK 500 ALA A 400 -147.51 43.88 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 A1001 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1630 O REMARK 620 2 HOH A1629 O 77.1 REMARK 620 3 HOH A1632 O 83.5 85.3 REMARK 620 4 HIS A 56 NE2 169.4 92.9 92.3 REMARK 620 5 HIS A 442 NE2 89.6 87.3 170.9 93.5 REMARK 620 6 HOH A1631 O 99.4 175.7 96.8 90.8 90.2 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 IOD A 1271 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 1284 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1001 DBREF 2NOO A 1 502 UNP P33590 NIKA_ECOLI 23 524 SEQADV 2NOO ALA A 22 UNP P33590 TYR 44 ENGINEERED SEQADV 2NOO ALA A 97 UNP P33590 ARG 119 ENGINEERED SEQADV 2NOO ALA A 100 UNP P33590 TRP 122 ENGINEERED SEQADV 2NOO ALA A 137 UNP P33590 ARG 159 ENGINEERED SEQADV 2NOO TYI A 300 UNP P33590 TYR 322 MODIFIED RESIDUE SEQADV 2NOO TYI A 382 UNP P33590 TYR 404 MODIFIED RESIDUE SEQADV 2NOO ALA A 398 UNP P33590 TRP 420 ENGINEERED SEQADV 2NOO ALA A 402 UNP P33590 TYR 424 ENGINEERED 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 ALA 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 ALA HIS ALA ALA 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 ALA 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 TYI 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 GLN 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 TYI ALA ARG GLN ARG ASP GLY ARG PHE SEQRES 31 A 502 GLY MET ILE PHE HIS ARG THR ALA GLY ALA PRO ALA 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 MODRES 2NOO TYI A 300 TYR 3,5-DIIODOTYROSINE MODRES 2NOO TYI A 382 TYR 3,5-DIIODOTYROSINE HET TYI A 300 14 HET TYI A 382 14 HET IOD A1271 1 HET IOD A1284 1 HET NI A1001 1 HETNAM TYI 3,5-DIIODOTYROSINE HETNAM IOD IODIDE ION HETNAM NI NICKEL (II) ION FORMUL 1 TYI 2(C9 H9 I2 N O3) FORMUL 2 IOD 2(I 1-) FORMUL 4 NI NI 2+ FORMUL 5 HOH *348(H2 O) HELIX 1 1 THR A 23 ASN A 25 5 3 HELIX 2 2 GLN A 26 TYR A 34 1 9 HELIX 3 3 ASP A 80 ASP A 93 1 14 HELIX 4 4 ASN A 94 ALA A 99 5 6 HELIX 5 5 LEU A 101 GLN A 106 1 6 HELIX 6 6 PRO A 128 ALA A 134 1 7 HELIX 7 7 ALA A 143 SER A 145 5 3 HELIX 8 8 ASP A 201 GLY A 212 1 12 HELIX 9 9 PRO A 225 ASN A 235 1 11 HELIX 10 10 GLU A 262 VAL A 273 1 12 HELIX 11 11 ASN A 274 LEU A 283 1 10 HELIX 12 12 ASP A 311 ALA A 322 1 12 HELIX 13 13 ASP A 350 GLN A 366 1 17 HELIX 14 14 GLU A 377 GLY A 388 1 12 HELIX 15 15 PRO A 404 ARG A 412 1 9 HELIX 16 16 HIS A 416 GLN A 422 1 7 HELIX 17 17 ASP A 427 THR A 441 1 15 HELIX 18 18 ASP A 443 GLU A 461 1 19 HELIX 19 19 PRO A 478 GLY A 481 5 4 HELIX 20 20 PRO A 493 ILE A 497 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 ASP A 176 O PHE A 196 SHEET 4 A 4 TRP A 165 LYS A 171 -1 N GLU A 169 O VAL A 177 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 LYS A 52 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 ALA A 112 -1 N ASP A 109 O THR A 121 SHEET 1 D 2 PHE A 147 LYS A 148 0 SHEET 2 D 2 GLU A 151 ILE A 156 -1 O GLU A 151 N LYS A 148 SHEET 1 E 3 LEU A 216 GLY A 219 0 SHEET 2 E 3 MET A 473 SER A 476 -1 O VAL A 475 N LEU A 217 SHEET 3 E 3 HIS A 239 LEU A 242 -1 N HIS A 239 O SER A 476 SHEET 1 F 6 GLN A 288 VAL A 289 0 SHEET 2 F 6 TYR A 464 TYR A 469 -1 O TYR A 469 N GLN A 288 SHEET 3 F 6 THR A 248 LEU A 253 -1 N VAL A 249 O SER A 468 SHEET 4 F 6 MET A 392 ARG A 396 -1 O HIS A 395 N MET A 250 SHEET 5 F 6 ARG A 341 ILE A 347 1 N GLU A 343 O MET A 392 SHEET 6 F 6 ASP A 370 GLU A 376 1 O SER A 372 N LEU A 344 SHEET 1 G 2 GLU A 334 LYS A 335 0 SHEET 2 G 2 GLN A 338 PRO A 339 -1 O GLN A 338 N LYS A 335 LINK C PRO A 299 N TYI A 300 1555 1555 1.33 LINK C TYI A 300 N ALA A 301 1555 1555 1.33 LINK C ILE A 381 N TYI A 382 1555 1555 1.33 LINK C TYI A 382 N ALA A 383 1555 1555 1.33 LINK NI NI A1001 O HOH A1630 1555 1555 2.24 LINK NI NI A1001 O HOH A1629 1555 1555 1.75 LINK NI NI A1001 O HOH A1632 1555 1555 2.17 LINK NI NI A1001 NE2 HIS A 56 1555 1555 2.04 LINK NI NI A1001 NE2 HIS A 442 1555 1555 2.05 LINK NI NI A1001 O HOH A1631 1555 1555 2.09 CISPEP 1 GLY A 15 PRO A 16 0 7.46 CISPEP 2 ALA A 137 PRO A 138 0 2.66 CISPEP 3 ALA A 258 PRO A 259 0 -4.37 CISPEP 4 ASP A 403 PRO A 404 0 0.63 SITE 1 AC1 2 TYR A 271 HOH A1318 SITE 1 AC2 2 ALA A 282 TYR A 284 SITE 1 AC3 6 HIS A 56 HIS A 442 HOH A1629 HOH A1630 SITE 2 AC3 6 HOH A1631 HOH A1632 CRYST1 43.470 92.248 116.383 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 0.023004 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010840 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008592 0.00000 MASTER 333 0 5 20 23 0 4 6 0 0 0 39 END