HEADER OXIDOREDUCTASE 26-JUN-24 9FUH TITLE CRYSTAL STRUCTURE OF REDUCED WILD TYPE THREE-DOMAIN HEME-CU NITRITE TITLE 2 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RALSTONIA PICKETTII; SOURCE 3 ORGANISM_TAXID: 329; SOURCE 4 GENE: NIRK, D7S62_04310; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-26 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 1 09-JUL-25 9FUH 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. 1.17 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) : 1.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 177460 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) : 0.122 REMARK 3 FREE R VALUE : 0.146 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.957 REMARK 3 FREE R VALUE TEST SET COUNT : 8797 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) : 1.17 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.20 REMARK 3 REFLECTION IN BIN (WORKING SET) : 12480 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.2810 REMARK 3 BIN FREE R VALUE SET COUNT : 697 REMARK 3 BIN FREE R VALUE : 0.2950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3423 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 711 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.11800 REMARK 3 B22 (A**2) : 0.11800 REMARK 3 B33 (A**2) : -0.38400 REMARK 3 B12 (A**2) : 0.05900 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): 0.027 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.028 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.024 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.298 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.987 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.982 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3795 ; 0.014 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3603 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5203 ; 1.883 ; 1.841 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8305 ; 0.690 ; 1.753 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 511 ; 7.016 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 19 ; 8.068 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 607 ;11.725 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 564 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4567 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 861 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 735 ; 0.240 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 143 ; 0.206 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1822 ; 0.180 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 532 ; 0.245 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.007 ; 0.200 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): 1 ; 0.038 ; 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): 1901 ; 3.838 ; 1.354 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1901 ; 3.816 ; 1.354 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2394 ; 5.209 ; 2.443 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2395 ; 5.216 ; 2.444 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1894 ; 6.157 ; 1.575 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1889 ; 6.148 ; 1.573 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2785 ; 8.583 ; 2.792 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2780 ; 8.577 ; 2.789 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): 7398 ; 3.963 ; 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 9FUH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1292131750. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-21 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 : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87000 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 : 177553 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.170 REMARK 200 RESOLUTION RANGE LOW (A) : 37.685 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 1.64200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 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 63.92100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.90481 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.77900 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 63.92100 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 36.90481 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.77900 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 63.92100 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 36.90481 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.77900 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 73.80961 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 57.55800 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 73.80961 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 57.55800 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 73.80961 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 57.55800 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: 18710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -276.0 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 -0.500000 -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 A1226 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1233 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1278 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1287 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1306 LIES ON A SPECIAL POSITION. 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 MET A 50 CG - SD - CE ANGL. DEV. = -11.2 DEGREES REMARK 500 GLU A 128 N - CA - CB ANGL. DEV. = -15.7 DEGREES REMARK 500 ARG A 197 CD - NE - CZ ANGL. DEV. = 12.0 DEGREES REMARK 500 ARG A 197 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 197 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 LEU A 235 CB - CG - CD2 ANGL. DEV. = 12.7 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 GLU A 252 -124.45 45.37 REMARK 500 THR A 363 -91.64 -117.14 REMARK 500 GLN A 369 154.10 82.93 REMARK 500 GLN A 369 156.28 79.20 REMARK 500 ASP A 391 83.14 -159.69 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 279 0.08 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 A1298 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A1299 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A1300 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A1301 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH A1302 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A1303 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A1304 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A1305 DISTANCE = 6.33 ANGSTROMS REMARK 525 HOH A1306 DISTANCE = 6.55 ANGSTROMS REMARK 525 HOH A1307 DISTANCE = 6.60 ANGSTROMS REMARK 525 HOH A1308 DISTANCE = 6.60 ANGSTROMS REMARK 525 HOH A1309 DISTANCE = 6.64 ANGSTROMS REMARK 525 HOH A1310 DISTANCE = 6.65 ANGSTROMS REMARK 525 HOH A1311 DISTANCE = 7.13 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 139.0 REMARK 620 3 HIS A 143 ND1 102.9 108.8 REMARK 620 4 MET A 148 SD 81.1 110.4 110.3 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 112.0 REMARK 620 3 HIS A 289 NE2 74.0 101.6 REMARK 620 4 HOH A 646 O 97.3 112.7 145.2 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 92.3 REMARK 620 3 HEC A 503 NB 87.2 90.5 REMARK 620 4 HEC A 503 NC 88.0 179.6 89.7 REMARK 620 5 HEC A 503 ND 92.1 89.2 179.2 90.7 REMARK 620 6 MET A 418 SD 177.7 85.4 92.4 94.3 88.3 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZIY RELATED DB: PDB DBREF 9FUH A 5 458 UNP I6NAW4 I6NAW4_RALPI 36 489 SEQRES 1 A 454 LEU PRO GLY ASP PHE GLY PRO PRO ARG GLY GLU PRO ILE SEQRES 2 A 454 HIS ALA VAL LEU THR SER PRO PRO LEU VAL PRO PRO PRO SEQRES 3 A 454 VAL ASN ARG THR TYR PRO ALA LYS VAL ILE VAL GLU LEU SEQRES 4 A 454 GLU VAL VAL GLU LYS GLU MET GLN ILE SER GLU GLY VAL SEQRES 5 A 454 SER TYR THR PHE TRP THR PHE GLY GLY THR VAL PRO GLY SEQRES 6 A 454 SER PHE ILE ARG VAL ARG GLN GLY ASP THR VAL GLU PHE SEQRES 7 A 454 HIS LEU LYS ASN HIS PRO SER SER LYS MET PRO HIS ASN SEQRES 8 A 454 ILE ASP LEU HIS GLY VAL THR GLY PRO GLY GLY GLY ALA SEQRES 9 A 454 ALA SER SER PHE THR ALA PRO GLY HIS GLU SER GLN PHE SEQRES 10 A 454 THR PHE LYS ALA LEU ASN GLU GLY ILE TYR VAL TYR HIS SEQRES 11 A 454 CYS ALA THR ALA PRO VAL GLY MET HIS ILE ALA ASN GLY SEQRES 12 A 454 MET TYR GLY LEU ILE LEU VAL GLU PRO PRO GLU GLY LEU SEQRES 13 A 454 PRO LYS VAL ASP HIS GLU TYR TYR VAL MET GLN GLY ASP SEQRES 14 A 454 PHE TYR THR ALA GLY LYS TYR ARG GLU LYS GLY LEU GLN SEQRES 15 A 454 PRO PHE ASP MET GLU LYS ALA ILE ASP GLU ARG PRO SER SEQRES 16 A 454 TYR VAL LEU PHE ASN GLY ALA GLU GLY ALA LEU THR GLY SEQRES 17 A 454 ASP LYS ALA LEU HIS ALA LYS VAL GLY GLU THR VAL ARG SEQRES 18 A 454 ILE PHE VAL GLY ASN GLY GLY PRO ASN LEU VAL SER SER SEQRES 19 A 454 PHE HIS VAL ILE GLY ALA ILE PHE ASP GLN VAL ARG TYR SEQRES 20 A 454 GLU GLY GLY THR ASN VAL GLN LYS ASN VAL GLN THR THR SEQRES 21 A 454 LEU ILE PRO ALA GLY GLY ALA ALA VAL VAL LYS PHE THR SEQRES 22 A 454 ALA ARG VAL PRO GLY SER TYR VAL LEU VAL ASP HIS SER SEQRES 23 A 454 ILE PHE ARG ALA PHE ASN LYS GLY ALA MET ALA ILE LEU SEQRES 24 A 454 LYS ILE ASP GLY ALA GLU ASN LYS LEU VAL TYR SER GLY SEQRES 25 A 454 LYS GLU LEU ASP SER VAL TYR LEU GLY ASP ARG ALA ALA SEQRES 26 A 454 PRO ASN MET SER ALA VAL THR LYS ALA THR GLN ALA SER SEQRES 27 A 454 VAL SER GLY THR LEU THR VAL GLN ASP GLN VAL GLN ALA SEQRES 28 A 454 GLY ARG ALA LEU PHE ALA GLY THR CYS SER VAL CYS HIS SEQRES 29 A 454 GLN GLY ASN GLY ALA GLY LEU PRO GLY VAL PHE PRO PRO SEQRES 30 A 454 LEU ALA LYS SER ASP PHE LEU ALA ALA ASP PRO LYS ARG SEQRES 31 A 454 ALA MET ASN ILE VAL LEU HIS GLY LEU ASN GLY LYS ILE SEQRES 32 A 454 LYS VAL ASN GLY GLN GLU TYR ASP SER VAL MET PRO PRO SEQRES 33 A 454 MET THR GLN LEU ASN ASP ASP GLU VAL ALA ASN ILE LEU SEQRES 34 A 454 THR TYR VAL LEU ASN SER TRP ASP ASN PRO GLY GLY ARG SEQRES 35 A 454 VAL SER ALA GLU ASP VAL LYS LYS VAL ARG ALA GLN HET CU A 501 1 HET CU A 502 1 HET HEC A 503 75 HET SO4 A 504 5 HETNAM CU COPPER (II) ION HETNAM HEC HEME C HETNAM SO4 SULFATE ION FORMUL 2 CU 2(CU 2+) FORMUL 4 HEC C34 H34 FE N4 O4 FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *711(H2 O) HELIX 1 AA1 GLY A 103 SER A 111 5 9 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 1.80 LINK SG ACYS A 367 CAC HEC A 503 1555 1555 1.86 LINK ND1 HIS A 94 CU CU A 501 1555 1555 2.00 LINK NE2 HIS A 99 CU CU A 502 1555 1555 2.01 LINK NE2 HIS A 134 CU CU A 502 1555 1555 1.99 LINK SG CYS A 135 CU CU A 501 1555 1555 2.20 LINK ND1 HIS A 143 CU CU A 501 1555 1555 2.05 LINK SD AMET A 148 CU CU A 501 1555 1555 2.65 LINK NE2 HIS A 289 CU CU A 502 1555 3555 1.99 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 CU A 502 O HOH A 646 1555 1555 2.02 CISPEP 1 PRO A 24 PRO A 25 0 3.97 CISPEP 2 VAL A 67 PRO A 68 0 -6.40 CISPEP 3 ALA A 138 PRO A 139 0 -7.69 CISPEP 4 GLY A 232 PRO A 233 0 17.38 CRYST1 127.842 127.842 86.337 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 0.007822 0.004516 0.000000 0.00000 SCALE2 0.000000 0.009032 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011583 0.00000 CONECT 1468 7187 CONECT 1551 7188 CONECT 2055 7188 CONECT 2067 7187 CONECT 2165 7187 CONECT 2234 7187 CONECT 5677 7211 CONECT 5727 7219 CONECT 5741 7189 CONECT 6552 7189 CONECT 7187 1468 2067 2165 2234 CONECT 7188 1551 2055 7317 CONECT 7189 5741 6552 7194 7205 CONECT 7189 7213 7221 CONECT 7190 7195 7225 7232 CONECT 7191 7198 7206 7233 CONECT 7192 7209 7214 7234 CONECT 7193 7217 7222 7235 CONECT 7194 7189 7195 7198 CONECT 7195 7190 7194 7196 CONECT 7196 7195 7197 7200 CONECT 7197 7196 7198 7199 CONECT 7198 7191 7194 7197 CONECT 7199 7197 7236 7237 7238 CONECT 7200 7196 7201 7239 7240 CONECT 7201 7200 7202 7241 7242 CONECT 7202 7201 7203 7204 CONECT 7203 7202 CONECT 7204 7202 CONECT 7205 7189 7206 7209 CONECT 7206 7191 7205 7207 CONECT 7207 7206 7208 7210 CONECT 7208 7207 7209 7211 CONECT 7209 7192 7205 7208 CONECT 7210 7207 7243 7244 7245 CONECT 7211 5677 7208 7212 7246 CONECT 7212 7211 7247 7248 7249 CONECT 7213 7189 7214 7217 CONECT 7214 7192 7213 7215 CONECT 7215 7214 7216 7218 CONECT 7216 7215 7217 7219 CONECT 7217 7193 7213 7216 CONECT 7218 7215 7250 7251 7252 CONECT 7219 5727 7216 7220 7253 CONECT 7220 7219 7254 7255 7256 CONECT 7221 7189 7222 7225 CONECT 7222 7193 7221 7223 CONECT 7223 7222 7224 7226 CONECT 7224 7223 7225 7227 CONECT 7225 7190 7221 7224 CONECT 7226 7223 7257 7258 7259 CONECT 7227 7224 7228 7260 7261 CONECT 7228 7227 7229 7262 7263 CONECT 7229 7228 7230 7231 CONECT 7230 7229 CONECT 7231 7229 CONECT 7232 7190 CONECT 7233 7191 CONECT 7234 7192 CONECT 7235 7193 CONECT 7236 7199 CONECT 7237 7199 CONECT 7238 7199 CONECT 7239 7200 CONECT 7240 7200 CONECT 7241 7201 CONECT 7242 7201 CONECT 7243 7210 CONECT 7244 7210 CONECT 7245 7210 CONECT 7246 7211 CONECT 7247 7212 CONECT 7248 7212 CONECT 7249 7212 CONECT 7250 7218 CONECT 7251 7218 CONECT 7252 7218 CONECT 7253 7219 CONECT 7254 7220 CONECT 7255 7220 CONECT 7256 7220 CONECT 7257 7226 CONECT 7258 7226 CONECT 7259 7226 CONECT 7260 7227 CONECT 7261 7227 CONECT 7262 7228 CONECT 7263 7228 CONECT 7264 7265 7266 7267 7268 CONECT 7265 7264 CONECT 7266 7264 CONECT 7267 7264 CONECT 7268 7264 CONECT 7317 7188 MASTER 403 0 4 14 25 0 0 6 4184 1 94 35 END