HEADER OXIDOREDUCTASE 15-JUN-18 6GT0 TITLE NITRITE-BOUND COPPER NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES TITLE 2 DETERMINED BY SERIAL FEMTOSECOND ROTATION CRYSTALLOGRAPHY COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER-CONTAINING NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CU-NIR; COMPND 5 EC: 1.7.2.1; COMPND 6 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_PLASMID: PET-26B(+) KEYWDS OXIDOREDUCTASE, FEMTOSECOND, SF-ROX, NITRITE REDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.P.HALSTED,K.YAMASHITA,C.C.GOPALASINGAM,R.T.SHENOY,K.HIRATA,H.AGO, AUTHOR 2 G.UENO,R.R.EADY,S.V.ANTONYUK,M.YAMAMOTO,S.S.HASNAIN REVDAT 2 31-JUL-19 6GT0 1 JRNL REVDAT 1 03-JUL-19 6GT0 0 JRNL AUTH T.P.HALSTED,K.YAMASHITA,C.C.GOPALASINGAM,R.T.SHENOY, JRNL AUTH 2 K.HIRATA,H.AGO,G.UENO,M.P.BLAKELEY,R.R.EADY,S.V.ANTONYUK, JRNL AUTH 3 M.YAMAMOTO,S.S.HASNAIN JRNL TITL CATALYTICALLY IMPORTANT DAMAGE-FREE STRUCTURES OF A COPPER JRNL TITL 2 NITRITE REDUCTASE OBTAINED BY FEMTOSECOND X-RAY LASER AND JRNL TITL 3 ROOM-TEMPERATURE NEUTRON CRYSTALLOGRAPHY. JRNL REF IUCRJ V. 6 761 2019 JRNL REFN ESSN 2052-2525 JRNL PMID 31316819 JRNL DOI 10.1107/S2052252519008285 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0230 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 43498 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) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2295 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3189 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2870 REMARK 3 BIN FREE R VALUE SET COUNT : 171 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2574 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 395 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.23 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): 0.068 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.069 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.049 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.341 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2707 ; 0.013 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 2383 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3673 ; 1.594 ; 1.672 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5578 ; 1.053 ; 1.640 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 351 ;21.215 ; 5.342 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 132 ;33.831 ;23.106 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 403 ;12.809 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;21.782 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 346 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3419 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 501 ; 0.001 ; 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): 1339 ; 1.289 ; 1.717 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1338 ; 1.287 ; 1.715 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1674 ; 1.852 ; 2.573 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1675 ; 1.851 ; 2.576 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1368 ; 2.524 ; 1.978 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1366 ; 2.472 ; 1.976 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1995 ; 3.584 ; 2.864 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2973 ; 4.666 ;21.808 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2868 ; 4.323 ;20.953 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 : NULL 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 6GT0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1200010510. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : BL2 REMARK 200 X-RAY GENERATOR MODEL : SACLA BEAMLINE BL2 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.242 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL 0.6.3 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45846 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 54.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 154.7 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 50.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M AMMONIUM SULPHATE, 100 MM REMARK 280 CITRATE BUFFER, PH 5.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.15K 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 47.46000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.46000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.46000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.46000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.46000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.46000 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 47.46000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 47.46000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 47.46000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 47.46000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 47.46000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 47.46000 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 47.46000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 47.46000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 47.46000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 47.46000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 47.46000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 47.46000 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: 16250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -104.0 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 47.46000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 1.000000 0.000000 47.46000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 0.000000 1.000000 -47.46000 REMARK 350 BIOMT3 3 -1.000000 0.000000 0.000000 47.46000 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 743 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 979 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 989 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 993 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 994 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 995 LIES ON A SPECIAL POSITION. 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 MET A -37 REMARK 465 THR A -36 REMARK 465 GLU A -35 REMARK 465 GLN A -34 REMARK 465 LEU A -33 REMARK 465 GLN A -32 REMARK 465 MET A -31 REMARK 465 THR A -30 REMARK 465 ARG A -29 REMARK 465 ARG A -28 REMARK 465 THR A -27 REMARK 465 MET A -26 REMARK 465 LEU A -25 REMARK 465 ALA A -24 REMARK 465 GLY A -23 REMARK 465 ALA A -22 REMARK 465 ALA A -21 REMARK 465 LEU A -20 REMARK 465 ALA A -19 REMARK 465 GLY A -18 REMARK 465 ALA A -17 REMARK 465 VAL A -16 REMARK 465 ALA A -15 REMARK 465 PRO A -14 REMARK 465 LEU A -13 REMARK 465 LEU A -12 REMARK 465 HIS A -11 REMARK 465 THR A -10 REMARK 465 ALA A -9 REMARK 465 GLN A -8 REMARK 465 ALA A -7 REMARK 465 HIS A -6 REMARK 465 ALA A -5 REMARK 465 ALA A -4 REMARK 465 GLY A -3 REMARK 465 ALA A -2 REMARK 465 ALA A -1 REMARK 465 ALA A 0 REMARK 465 ALA A 1 REMARK 465 ALA A 2 REMARK 465 GLY A 3 REMARK 465 ALA A 4 REMARK 465 ALA A 5 REMARK 465 PRO A 6 REMARK 465 VAL A 7 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 - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 250 NE - CZ - NH2 ANGL. DEV. = -3.6 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 69.69 -162.10 REMARK 500 LEU A 227 48.58 -102.09 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 307 141.25 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 993 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH A 994 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A 995 DISTANCE = 8.47 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 136.3 REMARK 620 3 HIS A 145 ND1 98.8 99.9 REMARK 620 4 MET A 150 SD 85.9 107.9 133.9 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 101.9 REMARK 620 3 NO2 A 503 N 125.3 121.1 REMARK 620 4 NO2 A 503 N 126.2 93.1 32.1 REMARK 620 5 NO2 A 503 O1 159.2 92.3 34.4 36.6 REMARK 620 6 NO2 A 503 O1 95.0 83.9 61.2 35.4 71.2 REMARK 620 7 NO2 A 503 O2 91.3 118.9 40.1 38.4 68.4 35.3 REMARK 620 8 NO2 A 503 O2 163.9 88.9 39.0 40.1 4.7 74.1 72.9 REMARK 620 9 HIS A 306 NE2 68.4 94.8 131.8 161.3 126.0 162.8 144.1 123.1 REMARK 620 N 1 2 3 4 5 6 7 8 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 NO2 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MLI A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MLI A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MLI A 507 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6GSQ RELATED DB: PDB REMARK 900 6GSQ CONTAINS THE RESTING STATE ENZYME. DBREF 6GT0 A -37 340 UNP P25006 NIR_ACHCY 1 378 SEQRES 1 A 378 MET THR GLU GLN LEU GLN MET THR ARG ARG THR MET LEU SEQRES 2 A 378 ALA GLY ALA ALA LEU ALA GLY ALA VAL ALA PRO LEU LEU SEQRES 3 A 378 HIS THR ALA GLN ALA HIS ALA ALA GLY ALA ALA ALA ALA SEQRES 4 A 378 ALA GLY ALA ALA PRO VAL ASP ILE SER THR LEU PRO ARG SEQRES 5 A 378 VAL LYS VAL ASP LEU VAL LYS PRO PRO PHE VAL HIS ALA SEQRES 6 A 378 HIS ASP GLN VAL ALA LYS THR GLY PRO ARG VAL VAL GLU SEQRES 7 A 378 PHE THR MET THR ILE GLU GLU LYS LYS LEU VAL ILE ASP SEQRES 8 A 378 ARG GLU GLY THR GLU ILE HIS ALA MET THR PHE ASN GLY SEQRES 9 A 378 SER VAL PRO GLY PRO LEU MET VAL VAL HIS GLU ASN ASP SEQRES 10 A 378 TYR VAL GLU LEU ARG LEU ILE ASN PRO ASP THR ASN THR SEQRES 11 A 378 LEU LEU HIS ASN ILE ASP PHE HIS ALA ALA THR GLY ALA SEQRES 12 A 378 LEU GLY GLY GLY ALA LEU THR GLN VAL ASN PRO GLY GLU SEQRES 13 A 378 GLU THR THR LEU ARG PHE LYS ALA THR LYS PRO GLY VAL SEQRES 14 A 378 PHE VAL TYR HIS CYS ALA PRO GLU GLY MET VAL PRO TRP SEQRES 15 A 378 HIS VAL THR SER GLY MET ASN GLY ALA ILE MET VAL LEU SEQRES 16 A 378 PRO ARG ASP GLY LEU LYS ASP GLU LYS GLY GLN PRO LEU SEQRES 17 A 378 THR TYR ASP LYS ILE TYR TYR VAL GLY GLU GLN ASP PHE SEQRES 18 A 378 TYR VAL PRO LYS ASP GLU ALA GLY ASN TYR LYS LYS TYR SEQRES 19 A 378 GLU THR PRO GLY GLU ALA TYR GLU ASP ALA VAL LYS ALA SEQRES 20 A 378 MET ARG THR LEU THR PRO THR HIS ILE VAL PHE ASN GLY SEQRES 21 A 378 ALA VAL GLY ALA LEU THR GLY ASP HIS ALA LEU THR ALA SEQRES 22 A 378 ALA VAL GLY GLU ARG VAL LEU VAL VAL HIS SER GLN ALA SEQRES 23 A 378 ASN ARG ASP THR ARG PRO HIS LEU ILE GLY GLY HIS GLY SEQRES 24 A 378 ASP TYR VAL TRP ALA THR GLY LYS PHE ARG ASN PRO PRO SEQRES 25 A 378 ASP LEU ASP GLN GLU THR TRP LEU ILE PRO GLY GLY THR SEQRES 26 A 378 ALA GLY ALA ALA PHE TYR THR PHE ARG GLN PRO GLY VAL SEQRES 27 A 378 TYR ALA TYR VAL ASN HIS ASN LEU ILE GLU ALA PHE GLU SEQRES 28 A 378 LEU GLY ALA ALA GLY HIS PHE LYS VAL THR GLY GLU TRP SEQRES 29 A 378 ASN ASP ASP LEU MET THR SER VAL VAL LYS PRO ALA SER SEQRES 30 A 378 MET HET CU A 501 1 HET CU A 502 1 HET NO2 A 503 6 HET SO4 A 504 5 HET MLI A 505 7 HET MLI A 506 7 HET MLI A 507 7 HETNAM CU COPPER (II) ION HETNAM NO2 NITRITE ION HETNAM SO4 SULFATE ION HETNAM MLI MALONATE ION FORMUL 2 CU 2(CU 2+) FORMUL 4 NO2 N O2 1- FORMUL 5 SO4 O4 S 2- FORMUL 6 MLI 3(C3 H2 O4 2-) FORMUL 9 HOH *395(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 THR A 120 N LEU A 85 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 LYS A 321 N LEU A 233 SHEET 3 AA6 4 GLY A 299 ASN A 305 -1 N GLY A 299 O VAL A 322 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 2.03 LINK NE2 HIS A 100 CU CU A 502 1555 1555 2.02 LINK NE2 HIS A 135 CU CU A 502 1555 1555 2.05 LINK SG CYS A 136 CU CU A 501 1555 1555 2.18 LINK ND1 HIS A 145 CU CU A 501 1555 1555 1.98 LINK SD MET A 150 CU CU A 501 1555 1555 2.44 LINK CU CU A 502 N ANO2 A 503 1555 1555 2.06 LINK CU CU A 502 N BNO2 A 503 1555 1555 2.08 LINK CU CU A 502 O1 ANO2 A 503 1555 1555 2.02 LINK CU CU A 502 O1 BNO2 A 503 1555 1555 2.02 LINK CU CU A 502 O2 ANO2 A 503 1555 1555 2.01 LINK CU CU A 502 O2 BNO2 A 503 1555 1555 1.99 LINK NE2 HIS A 306 CU CU A 502 1555 7555 2.01 CISPEP 1 PRO A 22 PRO A 23 0 10.17 CISPEP 2 VAL A 68 PRO A 69 0 -7.00 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 503 SITE 1 AC3 9 ASP A 98 HIS A 100 HIS A 135 HIS A 255 SITE 2 AC3 9 ILE A 257 HIS A 306 LEU A 308 CU A 502 SITE 3 AC3 9 HOH A 615 SITE 1 AC4 6 LYS A 33 ASP A 188 GLU A 189 LYS A 194 SITE 2 AC4 6 HOH A 778 HOH A 859 SITE 1 AC5 7 GLY A 225 PHE A 312 HIS A 319 HOH A 609 SITE 2 AC5 7 HOH A 629 HOH A 742 HOH A 776 SITE 1 AC6 6 ARG A 250 ASP A 251 ARG A 253 ASN A 307 SITE 2 AC6 6 GLU A 310 HOH A 646 SITE 1 AC7 4 THR A 228 GLY A 229 VAL A 300 HIS A 319 CRYST1 94.920 94.920 94.920 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 0.010535 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010535 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010535 0.00000