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 5 25-OCT-23 2NOO 1 REMARK REVDAT 4 10-NOV-21 2NOO 1 REMARK SEQADV LINK 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,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) : 1.65 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 HIS A 56 NE2 REMARK 620 2 HIS A 442 NE2 93.5 REMARK 620 3 HOH A1629 O 92.9 87.3 REMARK 620 4 HOH A1630 O 169.4 89.6 77.1 REMARK 620 5 HOH A1631 O 90.8 90.2 175.7 99.4 REMARK 620 6 HOH A1632 O 92.3 170.9 85.3 83.5 96.8 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 MUTATION SEQADV 2NOO ALA A 97 UNP P33590 ARG 119 ENGINEERED MUTATION SEQADV 2NOO ALA A 100 UNP P33590 TRP 122 ENGINEERED MUTATION SEQADV 2NOO ALA A 137 UNP P33590 ARG 159 ENGINEERED MUTATION 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 MUTATION SEQADV 2NOO ALA A 402 UNP P33590 TYR 424 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 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 NE2 HIS A 56 NI NI A1001 1555 1555 2.04 LINK NE2 HIS A 442 NI NI A1001 1555 1555 2.05 LINK NI NI A1001 O HOH A1629 1555 1555 1.75 LINK NI NI A1001 O HOH A1630 1555 1555 2.24 LINK NI NI A1001 O HOH A1631 1555 1555 2.09 LINK NI NI A1001 O HOH A1632 1555 1555 2.17 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