HEADER OXIDOREDUCTASE 31-JAN-24 8RV0 TITLE CRYSTAL STRUCTURE OF OCTAHEME NITRITE REDUCTASE FROM TRICHLOROBACTER TITLE 2 AMMONIFICANS IN COMPLEX WITH NITRITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: OCTAHEME CYTOCHROME C NITRITE REDUCTASE; COMPND 3 CHAIN: Y SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRICHLOROBACTER AMMONIFICANS; SOURCE 3 ORGANISM_TAXID: 2916410 KEYWDS OCTAHEME NITRITE REDUCTASE, COMPLEX WITH NITRITE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.M.POLYAKOV,T.N.SAFONOVA,E.OSIPOV,A.N.POPOV,T.V.TIKHONOVA,V.O.POPOV REVDAT 1 27-MAR-24 8RV0 0 JRNL AUTH K.M.POLYAKOV,T.N.SAFONOVA,E.OSIPOV,A.N.POPOV,T.V.TIKHONOVA, JRNL AUTH 2 V.O.POPOV JRNL TITL CRYSTAL STRUCTURE OF OCTAHEME NITRITE REDUCTASE FROM JRNL TITL 2 TRICHLOROBACTER AMMONIFICANS IN COMPLEX WITH NITRITE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 66322 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) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 3361 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4838 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.3540 REMARK 3 BIN FREE R VALUE SET COUNT : 318 REMARK 3 BIN FREE R VALUE : 0.3470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3891 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 350 REMARK 3 SOLVENT ATOMS : 450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.63000 REMARK 3 B22 (A**2) : -0.63000 REMARK 3 B33 (A**2) : 2.03000 REMARK 3 B12 (A**2) : -0.31000 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): 0.101 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.122 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.768 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4439 ; 0.022 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6097 ; 3.421 ; 1.803 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 494 ; 7.673 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 211 ;37.715 ;22.891 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 716 ;16.978 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;15.650 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 526 ; 0.227 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3461 ; 0.023 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1980 ; 3.444 ; 2.381 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2472 ; 4.314 ; 3.558 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2459 ; 4.090 ; 2.437 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): 7517 ; 6.582 ;32.117 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8RV0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1292134740. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-SEP-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96862 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 12M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69684 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 49.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 1.0 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM NANO2, 0.1 M BIS-TRIS, PH 5.7, REMARK 280 17-20 % PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+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 -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 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.61500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 32.61500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.61500 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: 38130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 53990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -598.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: Y 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 114.44000 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 57.22000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 99.10795 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 Y1066 LIES ON A SPECIAL POSITION. REMARK 375 HOH Y1126 LIES ON A SPECIAL POSITION. REMARK 375 HOH Y1137 LIES ON A SPECIAL POSITION. REMARK 375 HOH Y1145 LIES ON A SPECIAL POSITION. REMARK 375 HOH Y1148 LIES ON A SPECIAL POSITION. REMARK 375 HOH Y1150 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 CE2 TYR Y 312 SG CYS Y 314 1.73 REMARK 500 O HOH Y 960 O HOH Y 1037 1.81 REMARK 500 OE2 GLU Y 183 NH2 ARG Y 185 1.94 REMARK 500 OE1 GLN Y 456 O HOH Y 701 2.05 REMARK 500 O HOH Y 727 O HOH Y 1106 2.10 REMARK 500 NA HEC Y 604 O2 NO2 Y 610 2.10 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 CYS Y 423 CB CYS Y 423 SG -0.096 REMARK 500 GLU Y 437 CD GLU Y 437 OE2 -0.081 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 SER Y 51 N - CA - CB ANGL. DEV. = 10.9 DEGREES REMARK 500 ARG Y 185 CG - CD - NE ANGL. DEV. = 12.8 DEGREES REMARK 500 CYS Y 202 CA - CB - SG ANGL. DEV. = 7.1 DEGREES REMARK 500 CYS Y 388 CA - CB - SG ANGL. DEV. = 7.1 DEGREES REMARK 500 CYS Y 423 CA - CB - SG ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG Y 478 NE - CZ - NH2 ANGL. DEV. = -3.1 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 Y 112 -159.94 -125.18 REMARK 500 GLU Y 138 126.97 178.50 REMARK 500 ARG Y 143 -163.09 -128.02 REMARK 500 GLN Y 159 52.16 -155.86 REMARK 500 HIS Y 216 126.84 -35.50 REMARK 500 LEU Y 217 -2.69 75.44 REMARK 500 PRO Y 240 -173.86 -67.17 REMARK 500 VAL Y 241 128.26 -38.85 REMARK 500 ASP Y 268 56.62 -141.67 REMARK 500 ARG Y 288 24.56 48.59 REMARK 500 CYS Y 308 -40.36 -139.90 REMARK 500 CYS Y 314 44.81 -148.74 REMARK 500 HIS Y 370 71.11 20.92 REMARK 500 LYS Y 399 -127.08 47.95 REMARK 500 ASP Y 400 -74.93 -52.44 REMARK 500 MET Y 415 51.38 -148.98 REMARK 500 CYS Y 420 -52.06 -128.39 REMARK 500 GLN Y 465 -84.52 -60.38 REMARK 500 ARG Y 466 -39.46 -14.48 REMARK 500 GLU Y 467 51.55 -103.70 REMARK 500 PRO Y 471 -8.59 -60.00 REMARK 500 ASN Y 501 84.58 -163.11 REMARK 500 VAL Y 530 -77.80 -67.07 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 GLY Y 398 LYS Y 399 138.32 REMARK 500 GLU Y 467 GLY Y 468 -136.25 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 Y1149 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH Y1150 DISTANCE = 6.91 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 HEC Y 601 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS Y 46 NE2 REMARK 620 2 HEC Y 601 NA 90.4 REMARK 620 3 HEC Y 601 NB 96.7 90.1 REMARK 620 4 HEC Y 601 NC 90.2 178.5 88.4 REMARK 620 5 HEC Y 601 ND 82.3 88.2 178.0 93.2 REMARK 620 6 HIS Y 73 NE2 166.0 90.6 97.2 89.2 83.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC Y 603 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS Y 58 NE2 REMARK 620 2 HEC Y 603 NA 90.2 REMARK 620 3 HEC Y 603 NB 78.3 90.8 REMARK 620 4 HEC Y 603 NC 89.7 178.8 88.0 REMARK 620 5 HEC Y 603 ND 99.8 90.9 177.4 90.2 REMARK 620 6 HIS Y 95 NE2 167.3 84.7 90.1 95.1 91.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC Y 602 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS Y 67 NE2 REMARK 620 2 HEC Y 602 NA 86.4 REMARK 620 3 HEC Y 602 NB 90.0 101.0 REMARK 620 4 HEC Y 602 NC 92.2 170.7 88.2 REMARK 620 5 HEC Y 602 ND 88.6 77.1 177.7 93.7 REMARK 620 6 HIS Y 250 NE2 167.2 80.9 93.9 100.0 87.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC Y 606 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS Y 145 NE2 REMARK 620 2 HEC Y 606 NA 90.2 REMARK 620 3 HEC Y 606 NB 95.0 92.6 REMARK 620 4 HEC Y 606 NC 86.1 176.2 88.6 REMARK 620 5 HEC Y 606 ND 85.9 85.9 178.3 93.0 REMARK 620 6 HIS Y 309 NE2 175.5 94.1 83.4 89.7 95.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC Y 604 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS Y 206 NZ REMARK 620 2 HEC Y 604 NA 94.8 REMARK 620 3 HEC Y 604 NB 92.1 91.3 REMARK 620 4 HEC Y 604 NC 80.6 174.6 91.6 REMARK 620 5 HEC Y 604 ND 82.6 87.3 174.3 89.4 REMARK 620 6 NO Y 609 N 169.2 95.4 91.1 89.1 94.5 REMARK 620 7 NO2 Y 610 N 162.8 98.7 98.1 85.4 87.5 7.8 REMARK 620 8 NO2 Y 610 O2 157.5 62.9 85.8 121.9 98.4 33.1 38.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC Y 605 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS Y 247 NE2 REMARK 620 2 HEC Y 605 NA 89.8 REMARK 620 3 HEC Y 605 NB 90.4 89.2 REMARK 620 4 HEC Y 605 NC 86.2 175.9 90.7 REMARK 620 5 HEC Y 605 ND 89.6 90.1 179.2 90.0 REMARK 620 6 HIS Y 407 NE2 177.2 91.9 87.4 92.2 92.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA Y 611 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU Y 311 OE1 REMARK 620 2 GLU Y 311 OE2 51.8 REMARK 620 3 TYR Y 312 O 88.5 77.6 REMARK 620 4 LYS Y 367 O 86.5 101.3 174.4 REMARK 620 5 GLN Y 369 OE1 74.2 125.4 95.3 80.9 REMARK 620 6 HOH Y 912 O 157.3 148.5 88.9 94.7 83.7 REMARK 620 7 HOH Y 936 O 128.2 77.7 91.4 93.8 156.9 74.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC Y 608 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS Y 381 NE2 REMARK 620 2 HEC Y 608 NA 85.1 REMARK 620 3 HEC Y 608 NB 94.0 91.5 REMARK 620 4 HEC Y 608 NC 96.1 178.6 89.2 REMARK 620 5 HEC Y 608 ND 86.1 88.7 179.8 90.7 REMARK 620 6 HIS Y 424 NE2 179.1 94.6 86.9 84.2 93.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC Y 607 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS Y 392 NE2 REMARK 620 2 HEC Y 607 NA 83.3 REMARK 620 3 HEC Y 607 NB 89.5 90.4 REMARK 620 4 HEC Y 607 NC 89.2 172.4 90.7 REMARK 620 5 HEC Y 607 ND 86.7 89.5 176.2 88.9 REMARK 620 6 HIS Y 500 NE2 177.8 94.5 90.6 92.9 93.2 REMARK 620 N 1 2 3 4 5 DBREF 8RV0 Y 38 532 PDB 8RV0 8RV0 38 532 SEQRES 1 Y 495 GLY ARG GLU THR CYS TYR ALA CYS HIS THR GLU VAL LYS SEQRES 2 Y 495 SER LEU LYS GLU ASN SER LYS HIS ALA ALA ILE ALA CYS SEQRES 3 Y 495 THR VAL CYS HIS ASP LYS THR LYS GLU HIS LEU GLU LYS SEQRES 4 Y 495 GLY PRO ASP VAL LYS PRO VAL THR LYS ILE ASP GLN ALA SEQRES 5 Y 495 VAL CYS GLY SER CYS HIS LYS ASN GLN TYR GLU SER PHE SEQRES 6 Y 495 TYR ALA VAL HIS HIS ASP PRO THR GLY ALA ARG LYS GLU SEQRES 7 Y 495 LYS GLY ILE PRO ALA GLY ARG SER PRO LEU GLN ASP LYS SEQRES 8 Y 495 LEU LEU ALA GLY HIS GLY PHE THR PHE GLU HIS ALA GLU SEQRES 9 Y 495 PRO ARG GLY HIS ALA TYR MET VAL VAL ASP GLN PHE ALA SEQRES 10 Y 495 VAL ASP ARG PHE GLN GLY GLY ARG TYR GLN PHE LYS GLY SEQRES 11 Y 495 GLY TRP LYS ASN TYR ASP LYS VAL GLY LYS THR TRP ASP SEQRES 12 Y 495 ILE LEU GLU ASP ARG GLY PRO ASN ALA LYS LEU PRO GLU SEQRES 13 Y 495 THR ALA MET ALA GLY ASN PRO THR CYS ILE GLN CYS LYS SEQRES 14 Y 495 SER SER ASP LEU ILE LEU GLN TRP LYS HIS LEU GLY GLU SEQRES 15 Y 495 LYS GLY GLY LYS PHE ASP ARG THR SER ASN VAL ASN ASP SEQRES 16 Y 495 VAL VAL LYS ALA ILE ASN ASN PRO VAL GLY CYS ILE HIS SEQRES 17 Y 495 CYS HIS ASP PRO HIS GLY ALA GLN PRO ARG ILE VAL ARG SEQRES 18 Y 495 ASP GLY LEU ILE ALA ALA ILE GLU LYS ASP PRO ALA LYS SEQRES 19 Y 495 ASN ILE PHE ALA LYS ASN GLY LYS THR ASP LEU LYS VAL SEQRES 20 Y 495 ILE ASP PHE ARG GLY PHE ARG LYS ILE GLY VAL MET GLU SEQRES 21 Y 495 LYS THR ASP SER ARG MET MET CYS ALA GLN CYS HIS VAL SEQRES 22 Y 495 GLU TYR ASN CYS ASN PRO GLY THR GLN ARG THR ASP GLY SEQRES 23 Y 495 LYS PRO VAL THR PHE ALA ASP ALA ARG THR ASN HIS PHE SEQRES 24 Y 495 PRO LEU LYS ASN SER LEU GLN LEU LEU GLU HIS TYR ARG SEQRES 25 Y 495 SER ILE ASP PHE PHE ASP PHE LYS HIS ALA VAL THR GLY SEQRES 26 Y 495 ALA LYS LEU ILE LYS PHE GLN HIS PRO GLU ALA GLU THR SEQRES 27 Y 495 TYR ALA GLY SER ALA HIS ASP LYS ALA GLY VAL GLN CYS SEQRES 28 Y 495 HIS GLN CYS HIS MET PRO GLN VAL LYS GLY LYS ASP GLY SEQRES 29 Y 495 LYS LYS TYR SER THR HIS GLY VAL VAL LYS PRO ILE GLN SEQRES 30 Y 495 MET VAL GLN GLU SER CYS ILE SER CYS HIS LYS ASP TYR SEQRES 31 Y 495 THR PRO ASN LYS ALA LYS PHE MET ILE GLU THR ILE ARG SEQRES 32 Y 495 ASN TYR THR LYS GLY LYS MET ARG LYS SER GLU TYR TRP SEQRES 33 Y 495 LEU ALA GLN LEU ILE ASP THR PHE ALA VAL ALA GLN ARG SEQRES 34 Y 495 GLU GLY VAL SER PRO THR ILE LEU ASP GLN ALA ARG LEU SEQRES 35 Y 495 LYS HIS GLU GLU ALA HIS ALA LEU TRP GLU TYR TRP THR SEQRES 36 Y 495 ALA GLU ASN SER ASP GLY PHE HIS ASN PRO GLU GLN ALA SEQRES 37 Y 495 ARG GLN SER LEU THR GLY SER ILE SER ALA SER LYS ALA SEQRES 38 Y 495 GLY VAL LYS LEU LEU ASN ASP ALA ILE MET ALA VAL LYS SEQRES 39 Y 495 GLN HET HEC Y 601 43 HET HEC Y 602 43 HET HEC Y 603 43 HET HEC Y 604 43 HET HEC Y 605 43 HET HEC Y 606 43 HET HEC Y 607 43 HET HEC Y 608 43 HET NO Y 609 2 HET NO2 Y 610 3 HET CA Y 611 1 HETNAM HEC HEME C HETNAM NO NITRIC OXIDE HETNAM NO2 NITRITE ION HETNAM CA CALCIUM ION HETSYN NO NITROGEN MONOXIDE FORMUL 2 HEC 8(C34 H34 FE N4 O4) FORMUL 10 NO N O FORMUL 11 NO2 N O2 1- FORMUL 12 CA CA 2+ FORMUL 13 HOH *450(H2 O) HELIX 1 AA1 GLY Y 38 ALA Y 44 1 7 HELIX 2 AA2 HIS Y 46 GLU Y 54 1 9 HELIX 3 AA3 ALA Y 62 VAL Y 65 5 4 HELIX 4 AA4 LYS Y 69 LYS Y 76 1 8 HELIX 5 AA5 ASP Y 87 HIS Y 95 1 9 HELIX 6 AA6 HIS Y 95 ALA Y 104 1 10 HELIX 7 AA7 LEU Y 125 LEU Y 130 1 6 HELIX 8 AA8 HIS Y 133 PHE Y 137 5 5 HELIX 9 AA9 GLY Y 144 ALA Y 146 5 3 HELIX 10 AB1 TYR Y 147 VAL Y 155 1 9 HELIX 11 AB2 GLY Y 167 TYR Y 172 5 6 HELIX 12 AB3 LYS Y 177 ILE Y 181 1 5 HELIX 13 AB4 ASN Y 199 LYS Y 206 5 8 HELIX 14 AB5 LYS Y 215 GLU Y 219 5 5 HELIX 15 AB6 ASN Y 229 LYS Y 235 1 7 HELIX 16 AB7 GLY Y 242 CYS Y 246 5 5 HELIX 17 AB8 ARG Y 258 ASP Y 268 1 11 HELIX 18 AB9 ASP Y 300 ALA Y 306 1 7 HELIX 19 AC1 ASP Y 330 ASN Y 334 5 5 HELIX 20 AC2 GLN Y 343 ILE Y 351 1 9 HELIX 21 AC3 PRO Y 371 ALA Y 377 1 7 HELIX 22 AC4 SER Y 379 ALA Y 384 1 6 HELIX 23 AC5 GLN Y 387 MET Y 393 1 7 HELIX 24 AC6 LYS Y 411 GLN Y 414 5 4 HELIX 25 AC7 MET Y 415 CYS Y 420 1 6 HELIX 26 AC8 THR Y 428 GLU Y 467 1 40 HELIX 27 AC9 SER Y 470 GLU Y 494 1 25 HELIX 28 AD1 ASN Y 501 ALA Y 529 1 29 SHEET 1 AA1 2 HIS Y 67 ASP Y 68 0 SHEET 2 AA1 2 VAL Y 83 THR Y 84 -1 O VAL Y 83 N ASP Y 68 SHEET 1 AA2 2 TYR Y 163 PHE Y 165 0 SHEET 2 AA2 2 LEU Y 182 ASP Y 184 -1 O GLU Y 183 N GLN Y 164 SHEET 1 AA3 3 ARG Y 255 ILE Y 256 0 SHEET 2 AA3 3 ARG Y 291 VAL Y 295 -1 O GLY Y 294 N ILE Y 256 SHEET 3 AA3 3 LYS Y 283 PHE Y 287 -1 N PHE Y 287 O ARG Y 291 SHEET 1 AA4 2 GLY Y 317 THR Y 318 0 SHEET 2 AA4 2 PRO Y 325 VAL Y 326 -1 O VAL Y 326 N GLY Y 317 SHEET 1 AA5 2 PHE Y 356 LYS Y 357 0 SHEET 2 AA5 2 LYS Y 364 LEU Y 365 -1 O LEU Y 365 N PHE Y 356 SHEET 1 AA6 2 GLN Y 395 LYS Y 397 0 SHEET 2 AA6 2 LYS Y 403 SER Y 405 -1 O TYR Y 404 N VAL Y 396 LINK SG CYS Y 42 CAB HEC Y 601 1555 1555 1.69 LINK SG CYS Y 45 CAC HEC Y 601 1555 1555 1.83 LINK SG CYS Y 63 CAB HEC Y 602 1555 1555 1.79 LINK SG CYS Y 66 CAC HEC Y 602 1555 1555 1.85 LINK SG CYS Y 91 CAB HEC Y 603 1555 1555 1.79 LINK SG CYS Y 94 CAC HEC Y 603 1555 1555 1.85 LINK SG CYS Y 202 CAB HEC Y 604 1555 1555 1.81 LINK SG CYS Y 205 CAC HEC Y 604 1555 1555 1.81 LINK SG CYS Y 243 CAB HEC Y 605 1555 1555 1.76 LINK SG CYS Y 246 CAC HEC Y 605 1555 1555 1.84 LINK SG CYS Y 305 CAB HEC Y 606 1555 1555 1.74 LINK SG CYS Y 308 CAC HEC Y 606 1555 1555 1.73 LINK SG CYS Y 388 CAB HEC Y 607 1555 1555 1.76 LINK SG CYS Y 391 CAC HEC Y 607 1555 1555 1.81 LINK SG CYS Y 420 CAB HEC Y 608 1555 1555 1.71 LINK SG CYS Y 423 CAC HEC Y 608 1555 1555 1.82 LINK N NO Y 609 O1 NO2 Y 610 1555 1555 1.20 LINK NE2 HIS Y 46 FE HEC Y 601 1555 1555 1.99 LINK NE2 HIS Y 58 FE HEC Y 603 1555 1555 1.81 LINK NE2 HIS Y 67 FE HEC Y 602 1555 1555 1.96 LINK NE2 HIS Y 73 FE HEC Y 601 1555 1555 2.01 LINK NE2 HIS Y 95 FE HEC Y 603 1555 1555 1.93 LINK NE2 HIS Y 145 FE HEC Y 606 1555 1555 1.93 LINK NZ LYS Y 206 FE HEC Y 604 1555 1555 1.96 LINK NE2 HIS Y 247 FE HEC Y 605 1555 1555 1.93 LINK NE2 HIS Y 250 FE HEC Y 602 1555 1555 1.96 LINK NE2 HIS Y 309 FE HEC Y 606 1555 1555 1.93 LINK OE1 GLU Y 311 CA CA Y 611 1555 1555 2.56 LINK OE2 GLU Y 311 CA CA Y 611 1555 1555 2.56 LINK O TYR Y 312 CA CA Y 611 1555 1555 2.41 LINK O LYS Y 367 CA CA Y 611 1555 1555 2.28 LINK OE1 GLN Y 369 CA CA Y 611 1555 1555 2.30 LINK NE2 HIS Y 381 FE HEC Y 608 1555 1555 1.95 LINK NE2 HIS Y 392 FE HEC Y 607 1555 1555 1.97 LINK NE2 HIS Y 407 FE HEC Y 605 1555 1555 1.92 LINK NE2 HIS Y 424 FE HEC Y 608 1555 1555 1.89 LINK NE2 HIS Y 500 FE HEC Y 607 1555 1555 1.89 LINK FE HEC Y 604 N NO Y 609 1555 1555 1.93 LINK FE HEC Y 604 N NO2 Y 610 1555 1555 1.80 LINK FE HEC Y 604 O2 NO2 Y 610 1555 1555 1.96 LINK CA CA Y 611 O HOH Y 912 1555 1555 2.51 LINK CA CA Y 611 O HOH Y 936 1555 1555 2.39 CRYST1 114.440 114.440 65.230 90.00 90.00 120.00 P 63 6 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 0.008738 0.005045 0.000000 0.00000 SCALE2 0.000000 0.010090 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015330 0.00000