HEADER OXIDOREDUCTASE 26-JUN-24 9FUK TITLE CRYSTAL STRUCTURE OF NITRIC OXIDE-TREATED Q262N MUTANT OF THREE-DOMAIN TITLE 2 HEME-CU NITRITE REDUCTASE FROM RALSTONIA PICKETTII COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER-CONTAINING NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.7.2.1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RALSTONIA PICKETTII; SOURCE 3 ORGANISM_TAXID: 329; SOURCE 4 GENE: RPIC_4015; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HAEM AND CU CONTAINING NITRITE REDUCTASE, ELECTRON TRANSFER, REDOX KEYWDS 2 REACTIONS, METAL BINDING PROTEIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR N.PETCHYAM,S.ANTONYUK,S.S.HASNAIN REVDAT 2 17-DEC-25 9FUK 1 COMPND HET HETNAM HETSYN REVDAT 2 2 1 FORMUL LINK ATOM REVDAT 1 09-JUL-25 9FUK 0 JRNL AUTH N.PETCHYAM,S.ANTONYUK,S.S.HASNAIN JRNL TITL STRUCTURAL STUDIES OF HAEM THREE-DOMAIN COPPER NITRITE JRNL TITL 2 REDUCTASE MUTANTS FROM RALSTONIA PICKETTII JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 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) : 1.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 216270 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.107 REMARK 3 FREE R VALUE : 0.122 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.075 REMARK 3 FREE R VALUE TEST SET COUNT : 10975 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) : 1.09 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.12 REMARK 3 REFLECTION IN BIN (WORKING SET) : 12581 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE SET COUNT : 684 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3428 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 821 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.12700 REMARK 3 B22 (A**2) : -0.12700 REMARK 3 B33 (A**2) : 0.41200 REMARK 3 B12 (A**2) : -0.06300 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): 0.020 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.021 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.015 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.763 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.989 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.986 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4050 ; 0.010 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3863 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5608 ; 1.775 ; 1.847 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8999 ; 0.632 ; 1.762 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 580 ; 7.063 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 20 ; 8.715 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 678 ;11.149 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 609 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4939 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 929 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 747 ; 0.225 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 173 ; 0.233 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1907 ; 0.176 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 635 ; 0.221 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.133 ; 0.200 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): 1 ; 0.073 ; 0.200 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): 1994 ; 3.095 ; 1.208 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1994 ; 3.069 ; 1.208 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2534 ; 4.531 ; 2.184 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2535 ; 4.540 ; 2.186 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2056 ; 4.348 ; 1.388 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2054 ; 4.349 ; 1.389 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3016 ; 6.345 ; 2.471 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3016 ; 6.345 ; 2.470 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): 7913 ; 2.967 ; 3.000 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 : MASK BULK SOLVENT 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 USED IF PRESENT IN REMARK 3 THE INPUT FILE REMARK 4 REMARK 4 9FUK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1292131699. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 216270 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.090 REMARK 200 RESOLUTION RANGE LOW (A) : 37.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.2 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.90700 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: BROWN RED CRYSTAL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BIS-TRIS PROPANE PH 7.7, 200 MM REMARK 280 SODIUM CITRATE, AND 22% PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 64.03450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.97034 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.78400 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 64.03450 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 36.97034 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.78400 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 64.03450 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 36.97034 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.78400 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 73.94067 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 57.56800 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 73.94067 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 57.56800 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 73.94067 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 57.56800 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 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 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 A1314 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1318 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1379 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1382 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1393 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1415 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 4 CG CD CE NZ 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 PHE A 112 CB - CA - C ANGL. DEV. = 13.4 DEGREES REMARK 500 PHE A 112 CB - CA - C ANGL. DEV. = -12.6 DEGREES REMARK 500 MET A 190 CG - SD - CE ANGL. DEV. = 14.2 DEGREES REMARK 500 ARG A 197 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 279 NE - CZ - NH1 ANGL. DEV. = 3.9 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 ARG A 197 72.96 -119.45 REMARK 500 GLU A 252 -125.89 49.04 REMARK 500 ASP A 320 -158.49 -131.54 REMARK 500 ALA A 328 41.04 -91.88 REMARK 500 GLN A 369 155.63 78.99 REMARK 500 GLN A 369 157.00 76.81 REMARK 500 ASP A 391 76.30 -162.11 REMARK 500 ASP A 391 95.99 -162.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 13 0.09 SIDE CHAIN REMARK 500 ARG A 197 0.10 SIDE CHAIN 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 A1402 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A1403 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A1404 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A1405 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A1406 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A1407 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A1408 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A1409 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH A1410 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH A1411 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH A1412 DISTANCE = 6.46 ANGSTROMS REMARK 525 HOH A1413 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH A1414 DISTANCE = 6.55 ANGSTROMS REMARK 525 HOH A1415 DISTANCE = 6.56 ANGSTROMS REMARK 525 HOH A1416 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH A1417 DISTANCE = 6.62 ANGSTROMS REMARK 525 HOH A1418 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH A1419 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH A1420 DISTANCE = 6.84 ANGSTROMS REMARK 525 HOH A1421 DISTANCE = 7.96 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 94 ND1 REMARK 620 2 CYS A 135 SG 137.0 REMARK 620 3 HIS A 143 ND1 100.8 108.5 REMARK 620 4 MET A 148 SD 84.0 112.9 110.7 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 99 NE2 REMARK 620 2 HIS A 134 NE2 106.1 REMARK 620 3 HIS A 289 NE2 69.4 93.1 REMARK 620 4 HOH A 652 O 93.7 127.3 139.6 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 99 NE2 REMARK 620 2 HIS A 134 NE2 115.2 REMARK 620 3 HIS A 289 NE2 79.8 105.0 REMARK 620 4 HOH A 652 O 95.7 105.0 148.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 503 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 368 NE2 REMARK 620 2 HEC A 503 NA 91.5 REMARK 620 3 HEC A 503 NB 87.7 90.0 REMARK 620 4 HEC A 503 NC 89.1 179.3 90.0 REMARK 620 5 HEC A 503 ND 92.0 89.0 178.9 91.0 REMARK 620 6 MET A 418 SD 176.7 85.1 92.3 94.2 87.9 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZIY RELATED DB: PDB REMARK 900 3ZIY IS THE HEAM COPPER NITRITE REDUCTASE RELATED AS THE WILD TYPE REMARK 900 ENZYME DBREF 9FUK A 4 458 UNP B2UHR8 B2UHR8_RALPJ 35 489 SEQADV 9FUK ASN A 32 UNP B2UHR8 HIS 63 CONFLICT SEQADV 9FUK THR A 34 UNP B2UHR8 ASN 65 CONFLICT SEQADV 9FUK ASN A 262 UNP B2UHR8 GLN 293 ENGINEERED MUTATION SEQADV 9FUK MET A 300 UNP B2UHR8 LEU 331 CONFLICT SEQADV 9FUK ALA A 308 UNP B2UHR8 PRO 339 CONFLICT SEQADV 9FUK ASN A 310 UNP B2UHR8 SER 341 CONFLICT SEQADV 9FUK GLN A 340 UNP B2UHR8 GLU 371 CONFLICT SEQRES 1 A 455 LYS LEU PRO GLY ASP PHE GLY PRO PRO ARG GLY GLU PRO SEQRES 2 A 455 ILE HIS ALA VAL LEU THR SER PRO PRO LEU VAL PRO PRO SEQRES 3 A 455 PRO VAL ASN ARG THR TYR PRO ALA LYS VAL ILE VAL GLU SEQRES 4 A 455 LEU GLU VAL VAL GLU LYS GLU MET GLN ILE SER GLU GLY SEQRES 5 A 455 VAL SER TYR THR PHE TRP THR PHE GLY GLY THR VAL PRO SEQRES 6 A 455 GLY SER PHE ILE ARG VAL ARG GLN GLY ASP THR VAL GLU SEQRES 7 A 455 PHE HIS LEU LYS ASN HIS PRO SER SER LYS MET PRO HIS SEQRES 8 A 455 ASN ILE ASP LEU HIS GLY VAL THR GLY PRO GLY GLY GLY SEQRES 9 A 455 ALA ALA SER SER PHE THR ALA PRO GLY HIS GLU SER GLN SEQRES 10 A 455 PHE THR PHE LYS ALA LEU ASN GLU GLY ILE TYR VAL TYR SEQRES 11 A 455 HIS CYS ALA THR ALA PRO VAL GLY MET HIS ILE ALA ASN SEQRES 12 A 455 GLY MET TYR GLY LEU ILE LEU VAL GLU PRO PRO GLU GLY SEQRES 13 A 455 LEU PRO LYS VAL ASP HIS GLU TYR TYR VAL MET GLN GLY SEQRES 14 A 455 ASP PHE TYR THR ALA GLY LYS TYR ARG GLU LYS GLY LEU SEQRES 15 A 455 GLN PRO PHE ASP MET GLU LYS ALA ILE ASP GLU ARG PRO SEQRES 16 A 455 SER TYR VAL LEU PHE ASN GLY ALA GLU GLY ALA LEU THR SEQRES 17 A 455 GLY ASP LYS ALA LEU HIS ALA LYS VAL GLY GLU THR VAL SEQRES 18 A 455 ARG ILE PHE VAL GLY ASN GLY GLY PRO ASN LEU VAL SER SEQRES 19 A 455 SER PHE HIS VAL ILE GLY ALA ILE PHE ASP GLN VAL ARG SEQRES 20 A 455 TYR GLU GLY GLY THR ASN VAL GLN LYS ASN VAL ASN THR SEQRES 21 A 455 THR LEU ILE PRO ALA GLY GLY ALA ALA VAL VAL LYS PHE SEQRES 22 A 455 THR ALA ARG VAL PRO GLY SER TYR VAL LEU VAL ASP HIS SEQRES 23 A 455 SER ILE PHE ARG ALA PHE ASN LYS GLY ALA MET ALA ILE SEQRES 24 A 455 LEU LYS ILE ASP GLY ALA GLU ASN LYS LEU VAL TYR SER SEQRES 25 A 455 GLY LYS GLU LEU ASP SER VAL TYR LEU GLY ASP ARG ALA SEQRES 26 A 455 ALA PRO ASN MET SER ALA VAL THR LYS ALA THR GLN ALA SEQRES 27 A 455 SER VAL SER GLY THR LEU THR VAL GLN ASP GLN VAL GLN SEQRES 28 A 455 ALA GLY ARG ALA LEU PHE ALA GLY THR CYS SER VAL CYS SEQRES 29 A 455 HIS GLN GLY ASN GLY ALA GLY LEU PRO GLY VAL PHE PRO SEQRES 30 A 455 PRO LEU ALA LYS SER ASP PHE LEU ALA ALA ASP PRO LYS SEQRES 31 A 455 ARG ALA MET ASN ILE VAL LEU HIS GLY LEU ASN GLY LYS SEQRES 32 A 455 ILE LYS VAL ASN GLY GLN GLU TYR ASP SER VAL MET PRO SEQRES 33 A 455 PRO MET THR GLN LEU ASN ASP ASP GLU VAL ALA ASN ILE SEQRES 34 A 455 LEU THR TYR VAL LEU ASN SER TRP ASP ASN PRO GLY GLY SEQRES 35 A 455 ARG VAL SER ALA GLU ASP VAL LYS LYS VAL ARG ALA GLN HET CU A 501 1 HET CU A 502 2 HET HEC A 503 73 HETNAM CU COPPER (II) ION HETNAM HEC HEME C FORMUL 2 CU 2(CU 2+) FORMUL 4 HEC C34 H34 FE N4 O4 FORMUL 5 HOH *821(H2 O) HELIX 1 AA1 GLY A 103 PHE A 112 5 10 HELIX 2 AA2 PRO A 139 ASN A 146 1 8 HELIX 3 AA3 ASP A 189 ASP A 195 1 7 HELIX 4 AA4 THR A 211 ALA A 215 5 5 HELIX 5 AA5 SER A 290 LYS A 297 1 8 HELIX 6 AA6 ASP A 320 GLY A 325 1 6 HELIX 7 AA7 ASP A 326 ALA A 328 5 3 HELIX 8 AA8 MET A 332 GLY A 345 1 14 HELIX 9 AA9 THR A 348 ALA A 361 1 14 HELIX 10 AB1 CYS A 364 GLN A 369 1 6 HELIX 11 AB2 SER A 385 ASP A 391 1 7 HELIX 12 AB3 ASP A 391 GLY A 402 1 12 HELIX 13 AB4 ASN A 425 ASN A 438 1 14 HELIX 14 AB5 SER A 448 GLN A 458 1 11 SHEET 1 AA1 4 ILE A 17 HIS A 18 0 SHEET 2 AA1 4 LYS A 38 SER A 53 1 O ILE A 40 N ILE A 17 SHEET 3 AA1 4 THR A 79 ASN A 86 1 O HIS A 83 N VAL A 41 SHEET 4 AA1 4 GLU A 118 LYS A 124 -1 O PHE A 123 N VAL A 80 SHEET 1 AA2 4 ILE A 17 HIS A 18 0 SHEET 2 AA2 4 LYS A 38 SER A 53 1 O ILE A 40 N ILE A 17 SHEET 3 AA2 4 VAL A 56 PHE A 63 -1 O PHE A 60 N LYS A 48 SHEET 4 AA2 4 GLY A 184 LEU A 185 1 O GLY A 184 N SER A 57 SHEET 1 AA3 4 ILE A 72 ARG A 75 0 SHEET 2 AA3 4 TYR A 149 GLU A 155 1 O GLU A 155 N VAL A 74 SHEET 3 AA3 4 GLY A 129 HIS A 134 -1 N GLY A 129 O VAL A 154 SHEET 4 AA3 4 ASP A 97 LEU A 98 -1 N ASP A 97 O HIS A 134 SHEET 1 AA4 6 TYR A 200 PHE A 203 0 SHEET 2 AA4 6 HIS A 165 PHE A 174 -1 N PHE A 174 O TYR A 200 SHEET 3 AA4 6 THR A 223 GLY A 232 1 O PHE A 227 N TYR A 167 SHEET 4 AA4 6 ALA A 271 THR A 277 -1 O ALA A 272 N VAL A 228 SHEET 5 AA4 6 PHE A 246 TYR A 251 -1 N ARG A 250 O VAL A 273 SHEET 6 AA4 6 GLN A 258 VAL A 261 -1 O VAL A 261 N PHE A 246 SHEET 1 AA5 5 LEU A 216 LYS A 219 0 SHEET 2 AA5 5 MET A 300 ASP A 306 1 O LYS A 304 N LEU A 216 SHEET 3 AA5 5 GLY A 282 ASP A 288 -1 N GLY A 282 O ILE A 305 SHEET 4 AA5 5 SER A 237 ILE A 242 -1 N ILE A 242 O VAL A 285 SHEET 5 AA5 5 THR A 263 ILE A 266 -1 O THR A 264 N PHE A 239 SHEET 1 AA6 2 LEU A 403 VAL A 409 0 SHEET 2 AA6 2 GLN A 412 MET A 418 -1 O MET A 418 N LEU A 403 LINK SG CYS A 364 CAB HEC A 503 1555 1555 1.82 LINK SG CYS A 367 CAC HEC A 503 1555 1555 1.85 LINK ND1 HIS A 94 CU CU A 501 1555 1555 2.03 LINK NE2 HIS A 99 CU B CU A 502 1555 1555 2.25 LINK NE2 HIS A 99 CU A CU A 502 1555 1555 1.87 LINK NE2 HIS A 134 CU B CU A 502 1555 1555 1.91 LINK NE2 HIS A 134 CU A CU A 502 1555 1555 2.07 LINK SG CYS A 135 CU CU A 501 1555 1555 2.21 LINK ND1 HIS A 143 CU CU A 501 1555 1555 2.06 LINK SD MET A 148 CU CU A 501 1555 1555 2.56 LINK NE2 HIS A 289 CU B CU A 502 1555 3555 2.19 LINK NE2 HIS A 289 CU A CU A 502 1555 3555 1.96 LINK NE2 HIS A 368 FE HEC A 503 1555 1555 2.00 LINK SD MET A 418 FE HEC A 503 1555 1555 2.33 LINK CU A CU A 502 O HOH A 652 1555 1555 2.17 LINK CU B CU A 502 O HOH A 652 1555 1555 1.85 CISPEP 1 PRO A 24 PRO A 25 0 3.44 CISPEP 2 VAL A 67 PRO A 68 0 -6.80 CISPEP 3 ALA A 138 PRO A 139 0 -11.26 CISPEP 4 GLY A 232 PRO A 233 0 19.55 CRYST1 128.069 128.069 86.352 90.00 90.00 120.00 H 3 9 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 0.007808 0.004508 0.000000 0.00000 SCALE2 0.000000 0.009016 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011581 0.00000 CONECT 1496 7665 CONECT 1579 7666 7667 CONECT 2138 7666 7667 CONECT 2150 7665 CONECT 2247 7665 CONECT 2313 7665 CONECT 6085 7690 CONECT 6133 7698 CONECT 6147 7668 CONECT 6977 7668 CONECT 7665 1496 2150 2247 2313 CONECT 7666 1579 2138 7796 CONECT 7667 1579 2138 7796 CONECT 7668 6147 6977 7673 7684 CONECT 7668 7692 7700 CONECT 7669 7674 7704 7711 CONECT 7670 7677 7685 7712 CONECT 7671 7688 7693 7713 CONECT 7672 7696 7701 7714 CONECT 7673 7668 7674 7677 CONECT 7674 7669 7673 7675 CONECT 7675 7674 7676 7679 CONECT 7676 7675 7677 7678 CONECT 7677 7670 7673 7676 CONECT 7678 7676 7715 7716 7717 CONECT 7679 7675 7680 7718 7719 CONECT 7680 7679 7681 7720 7721 CONECT 7681 7680 7682 7683 CONECT 7682 7681 CONECT 7683 7681 CONECT 7684 7668 7685 7688 CONECT 7685 7670 7684 7686 CONECT 7686 7685 7687 7689 CONECT 7687 7686 7688 7690 CONECT 7688 7671 7684 7687 CONECT 7689 7686 7722 7723 7724 CONECT 7690 6085 7687 7691 7725 CONECT 7691 7690 7726 7727 CONECT 7692 7668 7693 7696 CONECT 7693 7671 7692 7694 CONECT 7694 7693 7695 7697 CONECT 7695 7694 7696 7698 CONECT 7696 7672 7692 7695 CONECT 7697 7694 7728 7729 7730 CONECT 7698 6133 7695 7699 7731 CONECT 7699 7698 7732 7733 CONECT 7700 7668 7701 7704 CONECT 7701 7672 7700 7702 CONECT 7702 7701 7703 7705 CONECT 7703 7702 7704 7706 CONECT 7704 7669 7700 7703 CONECT 7705 7702 7734 7735 7736 CONECT 7706 7703 7707 7737 7738 CONECT 7707 7706 7708 7739 7740 CONECT 7708 7707 7709 7710 CONECT 7709 7708 CONECT 7710 7708 CONECT 7711 7669 CONECT 7712 7670 CONECT 7713 7671 CONECT 7714 7672 CONECT 7715 7678 CONECT 7716 7678 CONECT 7717 7678 CONECT 7718 7679 CONECT 7719 7679 CONECT 7720 7680 CONECT 7721 7680 CONECT 7722 7689 CONECT 7723 7689 CONECT 7724 7689 CONECT 7725 7690 CONECT 7726 7691 CONECT 7727 7691 CONECT 7728 7697 CONECT 7729 7697 CONECT 7730 7697 CONECT 7731 7698 CONECT 7732 7699 CONECT 7733 7699 CONECT 7734 7705 CONECT 7735 7705 CONECT 7736 7705 CONECT 7737 7706 CONECT 7738 7706 CONECT 7739 7707 CONECT 7740 7707 CONECT 7796 7666 7667 MASTER 425 0 3 14 25 0 0 6 4294 1 88 35 END