HEADER OXIDOREDUCTASE 16-FEB-16 5I6L TITLE CRYSTAL STRUCTURE OF COPPER NITRITE REDUCTASE AT 100K AFTER 2.76 MGY COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER-CONTAINING NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: COPPER NITRITE REDUCTASE; COMPND 5 SYNONYM: CU-NIR; COMPND 6 EC: 1.7.2.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACHROMOBACTER CYCLOCLASTES; SOURCE 3 ORGANISM_TAXID: 223; SOURCE 4 GENE: NIRK; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-26B(+) KEYWDS COPPER NITRITE REDUCTASE, REACTION MECHANISM, SERIAL CRYSTALLOGRAPHY, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.HORRELL,M.A.HOUGH,R.W.STRANGE REVDAT 6 10-JAN-24 5I6L 1 LINK REVDAT 5 30-AUG-17 5I6L 1 REMARK REVDAT 4 28-SEP-16 5I6L 1 JRNL REVDAT 3 21-SEP-16 5I6L 1 JRNL REVDAT 2 27-JUL-16 5I6L 1 JRNL REVDAT 1 13-JUL-16 5I6L 0 JRNL AUTH S.HORRELL,S.V.ANTONYUK,R.R.EADY,S.S.HASNAIN,M.A.HOUGH, JRNL AUTH 2 R.W.STRANGE JRNL TITL SERIAL CRYSTALLOGRAPHY CAPTURES ENZYME CATALYSIS IN COPPER JRNL TITL 2 NITRITE REDUCTASE AT ATOMIC RESOLUTION FROM ONE CRYSTAL. JRNL REF IUCRJ V. 3 271 2016 JRNL REFN ESSN 2052-2525 JRNL PMID 27437114 JRNL DOI 10.1107/S205225251600823X REMARK 2 REMARK 2 RESOLUTION. 1.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 113309 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) : 0.120 REMARK 3 R VALUE (WORKING SET) : 0.119 REMARK 3 FREE R VALUE : 0.141 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5926 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) : 1.08 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.11 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8095 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE SET COUNT : 401 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2566 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 345 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.025 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.026 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.018 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.864 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.983 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.978 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2853 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2644 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3872 ; 1.738 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6109 ; 1.017 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 359 ; 7.869 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 130 ;34.951 ;24.462 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 445 ;11.802 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;18.013 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 421 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3243 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 635 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1410 ; 1.238 ; 1.147 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1408 ; 1.192 ; 1.144 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1765 ; 1.549 ; 1.731 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 5494 ; 2.016 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 69 ;26.423 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5696 ; 7.891 ; 5.000 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 : 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5I6L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000218361. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.17 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 119248 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.080 REMARK 200 RESOLUTION RANGE LOW (A) : 42.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.86400 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: REFMAC REMARK 200 STARTING MODEL: 2BWI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.7 M AMMONIUM SULPHATE, 0.1 M SODIUM REMARK 280 ACETATE PH 4.5, EVAPORATION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 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 47.64950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.64950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.64950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.64950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.64950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.64950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 47.64950 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 47.64950 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 47.64950 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 47.64950 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 47.64950 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 47.64950 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 47.64950 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 47.64950 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 47.64950 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 47.64950 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 47.64950 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 47.64950 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 16540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 753 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 929 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 940 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 944 LIES ON A SPECIAL POSITION. 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 O TYR A 193 O HOH A 601 2.11 REMARK 500 REMARK 500 REMARK: NULL 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 TYR A 193 C LYS A 194 N -0.214 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 123 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 211 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 253 NE - CZ - NH2 ANGL. DEV. = -3.0 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 ALA A 137 68.21 -156.23 REMARK 500 MET A 141 34.59 -141.81 REMARK 500 ASP A 205 -14.60 147.59 REMARK 500 LEU A 213 19.52 59.83 REMARK 500 LEU A 227 46.63 -101.44 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 HIS A 306 ASN A 307 142.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 945 DISTANCE = 6.09 ANGSTROMS 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 CU A 501 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 ND1 REMARK 620 2 CYS A 136 SG 128.7 REMARK 620 3 HIS A 145 ND1 100.7 108.2 REMARK 620 4 MET A 150 SD 86.0 107.2 127.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 502 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 100 NE2 REMARK 620 2 HIS A 135 NE2 108.5 REMARK 620 3 HIS A 306 NE2 70.5 93.5 REMARK 620 4 NO2 A 505 N 115.4 119.0 139.5 REMARK 620 5 NO2 A 505 O1 93.3 105.6 158.3 35.4 REMARK 620 6 NO2 A 505 O2 154.1 93.3 123.2 39.2 66.8 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 CU A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MLI A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO2 A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO2 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO2 A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO2 A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO2 A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO2 A 510 DBREF 5I6L A 8 339 UNP P25006 NIR_ACHCY 46 377 SEQRES 1 A 332 ASP ILE SER THR LEU PRO ARG VAL LYS VAL ASP LEU VAL SEQRES 2 A 332 LYS PRO PRO PHE VAL HIS ALA HIS ASP GLN VAL ALA LYS SEQRES 3 A 332 THR GLY PRO ARG VAL VAL GLU PHE THR MET THR ILE GLU SEQRES 4 A 332 GLU LYS LYS LEU VAL ILE ASP ARG GLU GLY THR GLU ILE SEQRES 5 A 332 HIS ALA MET THR PHE ASN GLY SER VAL PRO GLY PRO LEU SEQRES 6 A 332 MET VAL VAL HIS GLU ASN ASP TYR VAL GLU LEU ARG LEU SEQRES 7 A 332 ILE ASN PRO ASP THR ASN THR LEU LEU HIS ASN ILE ASP SEQRES 8 A 332 PHE HIS ALA ALA THR GLY ALA LEU GLY GLY GLY ALA LEU SEQRES 9 A 332 THR GLN VAL ASN PRO GLY GLU GLU THR THR LEU ARG PHE SEQRES 10 A 332 LYS ALA THR LYS PRO GLY VAL PHE VAL TYR HIS CYS ALA SEQRES 11 A 332 PRO GLU GLY MET VAL PRO TRP HIS VAL THR SER GLY MET SEQRES 12 A 332 ASN GLY ALA ILE MET VAL LEU PRO ARG ASP GLY LEU LYS SEQRES 13 A 332 ASP GLU LYS GLY GLN PRO LEU THR TYR ASP LYS ILE TYR SEQRES 14 A 332 TYR VAL GLY GLU GLN ASP PHE TYR VAL PRO LYS ASP GLU SEQRES 15 A 332 ALA GLY ASN TYR LYS LYS TYR GLU THR PRO GLY GLU ALA SEQRES 16 A 332 TYR GLU ASP ALA VAL LYS ALA MET ARG THR LEU THR PRO SEQRES 17 A 332 THR HIS ILE VAL PHE ASN GLY ALA VAL GLY ALA LEU THR SEQRES 18 A 332 GLY ASP HIS ALA LEU THR ALA ALA VAL GLY GLU ARG VAL SEQRES 19 A 332 LEU VAL VAL HIS SER GLN ALA ASN ARG ASP THR ARG PRO SEQRES 20 A 332 HIS LEU ILE GLY GLY HIS GLY ASP TYR VAL TRP ALA THR SEQRES 21 A 332 GLY LYS PHE ARG ASN PRO PRO ASP LEU ASP GLN GLU THR SEQRES 22 A 332 TRP LEU ILE PRO GLY GLY THR ALA GLY ALA ALA PHE TYR SEQRES 23 A 332 THR PHE ARG GLN PRO GLY VAL TYR ALA TYR VAL ASN HIS SEQRES 24 A 332 ASN LEU ILE GLU ALA PHE GLU LEU GLY ALA ALA GLY HIS SEQRES 25 A 332 PHE LYS VAL THR GLY GLU TRP ASN ASP ASP LEU MET THR SEQRES 26 A 332 SER VAL VAL LYS PRO ALA SER HET CU A 501 1 HET CU A 502 1 HET ACT A 503 4 HET MLI A 504 7 HET NO2 A 505 3 HET NO2 A 506 3 HET NO2 A 507 3 HET NO2 A 508 3 HET NO2 A 509 3 HET NO2 A 510 3 HETNAM CU COPPER (II) ION HETNAM ACT ACETATE ION HETNAM MLI MALONATE ION HETNAM NO2 NITRITE ION FORMUL 2 CU 2(CU 2+) FORMUL 4 ACT C2 H3 O2 1- FORMUL 5 MLI C3 H2 O4 2- FORMUL 6 NO2 6(N O2 1-) FORMUL 12 HOH *345(H2 O) HELIX 1 AA1 ASP A 8 LEU A 12 5 5 HELIX 2 AA2 GLY A 104 THR A 112 5 9 HELIX 3 AA3 MET A 141 SER A 148 1 8 HELIX 4 AA4 THR A 198 THR A 212 1 15 HELIX 5 AA5 THR A 228 ALA A 232 5 5 HELIX 6 AA6 ASN A 307 GLU A 313 1 7 SHEET 1 AA1 3 ARG A 14 LYS A 16 0 SHEET 2 AA1 3 VAL A 38 VAL A 51 1 O GLU A 40 N VAL A 15 SHEET 3 AA1 3 GLU A 58 PHE A 64 -1 O ALA A 61 N LYS A 48 SHEET 1 AA2 4 ARG A 14 LYS A 16 0 SHEET 2 AA2 4 VAL A 38 VAL A 51 1 O GLU A 40 N VAL A 15 SHEET 3 AA2 4 TYR A 80 ASN A 87 1 O TYR A 80 N VAL A 39 SHEET 4 AA2 4 GLU A 118 LYS A 125 -1 O PHE A 124 N VAL A 81 SHEET 1 AA3 4 LEU A 72 HIS A 76 0 SHEET 2 AA3 4 ASN A 151 LEU A 157 1 O MET A 155 N MET A 73 SHEET 3 AA3 4 GLY A 130 HIS A 135 -1 N GLY A 130 O VAL A 156 SHEET 4 AA3 4 ASP A 98 PHE A 99 -1 N ASP A 98 O HIS A 135 SHEET 1 AA4 2 LEU A 162 LYS A 163 0 SHEET 2 AA4 2 PRO A 169 LEU A 170 -1 O LEU A 170 N LEU A 162 SHEET 1 AA5 6 HIS A 217 PHE A 220 0 SHEET 2 AA5 6 LYS A 174 PHE A 183 -1 N GLN A 181 O VAL A 219 SHEET 3 AA5 6 ARG A 240 GLN A 247 1 O VAL A 244 N VAL A 178 SHEET 4 AA5 6 THR A 287 THR A 294 -1 O TYR A 293 N VAL A 241 SHEET 5 AA5 6 GLY A 261 TRP A 265 -1 N TYR A 263 O PHE A 292 SHEET 6 AA5 6 ASP A 275 GLN A 278 -1 O ASP A 275 N VAL A 264 SHEET 1 AA6 4 LEU A 233 ALA A 236 0 SHEET 2 AA6 4 ALA A 317 THR A 323 1 O HIS A 319 N LEU A 233 SHEET 3 AA6 4 GLY A 299 ASN A 305 -1 N TYR A 303 O GLY A 318 SHEET 4 AA6 4 PRO A 254 ILE A 257 -1 N ILE A 257 O ALA A 302 LINK ND1 HIS A 95 CU CU A 501 1555 1555 2.04 LINK NE2 HIS A 100 CU CU A 502 1555 1555 2.03 LINK NE2 HIS A 135 CU CU A 502 1555 1555 2.06 LINK SG CYS A 136 CU CU A 501 1555 1555 2.21 LINK ND1 HIS A 145 CU CU A 501 1555 1555 2.03 LINK SD MET A 150 CU CU A 501 1555 1555 2.49 LINK NE2 HIS A 306 CU CU A 502 1555 5555 2.03 LINK CU CU A 502 N NO2 A 505 1555 1555 1.92 LINK CU CU A 502 O1 NO2 A 505 1555 1555 2.03 LINK CU CU A 502 O2 NO2 A 505 1555 1555 2.14 CISPEP 1 PRO A 22 PRO A 23 0 12.73 CISPEP 2 VAL A 68 PRO A 69 0 -6.72 SITE 1 AC1 4 HIS A 95 CYS A 136 HIS A 145 MET A 150 SITE 1 AC2 4 HIS A 100 HIS A 135 HIS A 306 NO2 A 505 SITE 1 AC3 4 THR A 228 GLY A 229 HIS A 319 LYS A 321 SITE 1 AC4 4 GLY A 225 PHE A 312 HOH A 687 HOH A 754 SITE 1 AC5 10 ASP A 98 HIS A 100 HIS A 135 HIS A 255 SITE 2 AC5 10 ILE A 257 HIS A 306 LEU A 308 CU A 502 SITE 3 AC5 10 HOH A 645 HOH A 712 SITE 1 AC6 4 ARG A 250 ASP A 251 ARG A 253 NO2 A 510 SITE 1 AC7 4 THR A 171 ARG A 240 HOH A 618 HOH A 852 SITE 1 AC8 8 TRP A 265 THR A 267 GLY A 268 LYS A 269 SITE 2 AC8 8 ASN A 272 GLN A 278 HOH A 626 HOH A 644 SITE 1 AC9 3 LYS A 125 ARG A 296 HOH A 703 SITE 1 AD1 6 ARG A 250 ARG A 253 ASN A 307 GLU A 310 SITE 2 AD1 6 NO2 A 506 HOH A 604 CRYST1 95.299 95.299 95.299 90.00 90.00 90.00 P 21 3 12 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 0.010493 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010493 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010493 0.00000