HEADER OXIDOREDUCTASE 02-MAR-17 5NC0 TITLE THE 0.91 A RESOLUTION STRUCTURE OF THE L16G MUTANT OF CYTOCHROME C TITLE 2 PRIME FROM ALCALIGENES XYLOSOXIDANS, COMPLEXED WITH NITRIC OXIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: RESIDUE PCA IS PYROGLUTAMIC ACID - 2-PYRROLIDONE-5- COMPND 7 CARBOXYLIC ACID SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ALCALIGENES XYLOSOXYDANS XYLOSOXYDANS; SOURCE 3 ORGANISM_TAXID: 85698; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NITRIC OXIDE, CYTOCHROME, HOMODIMER, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR R.STRANGE,M.HOUGH,S.ANTONYUK,N.RUSTAGE REVDAT 4 06-NOV-24 5NC0 1 REMARK REVDAT 3 17-JAN-24 5NC0 1 REMARK REVDAT 2 11-MAR-20 5NC0 1 SEQRES REVDAT 1 10-JAN-18 5NC0 0 JRNL AUTH Z.N.NILSSON,B.L.MANDELLA,K.SEN,D.KEKILLI,M.A.HOUGH, JRNL AUTH 2 P.MOENNE-LOCCOZ,R.W.STRANGE,C.R.ANDREW JRNL TITL DISTINGUISHING NITRO VS NITRITO COORDINATION IN CYTOCHROME JRNL TITL 2 C' USING VIBRATIONAL SPECTROSCOPY AND DENSITY FUNCTIONAL JRNL TITL 3 THEORY. JRNL REF INORG CHEM V. 56 13205 2017 JRNL REFN ISSN 1520-510X JRNL PMID 29053273 JRNL DOI 10.1021/ACS.INORGCHEM.7B01945 REMARK 2 REMARK 2 RESOLUTION. 0.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 0.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.07 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 101466 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) : 0.125 REMARK 3 R VALUE (WORKING SET) : 0.125 REMARK 3 FREE R VALUE : 0.132 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5378 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) : 0.91 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 0.93 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7086 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.31 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 359 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 936 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 87 REMARK 3 SOLVENT ATOMS : 230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.15000 REMARK 3 B22 (A**2) : -0.15000 REMARK 3 B33 (A**2) : 0.48000 REMARK 3 B12 (A**2) : -0.07000 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): 0.014 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.014 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.010 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.378 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.978 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1091 ; 0.018 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 991 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1484 ; 2.471 ; 2.077 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2306 ; 1.075 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 138 ; 4.750 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 41 ;30.774 ;24.390 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 170 ;11.017 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;11.307 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 149 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1264 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 209 ; 0.002 ; 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): 521 ; 0.716 ; 0.598 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 518 ; 0.623 ; 0.593 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 653 ; 0.976 ; 0.900 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 654 ; 0.984 ; 0.904 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 570 ; 1.530 ; 0.839 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 570 ; 1.530 ; 0.839 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 827 ; 1.816 ; 1.169 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1366 ; 2.578 ; 9.424 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1367 ; 2.577 ; 9.430 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2081 ; 5.075 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 156 ;19.653 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2149 ; 6.354 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 5NC0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1200003862. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-SEP-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.78720 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20161101 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 106845 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.910 REMARK 200 RESOLUTION RANGE LOW (A) : 44.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC 5.8.0158 REMARK 200 STARTING MODEL: 2YL7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULPHATE, TRIS PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 122.16667 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 61.08333 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 91.62500 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 30.54167 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 152.70833 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 122.16667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 61.08333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 30.54167 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 91.62500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 152.70833 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -141.0 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 30.54167 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 LYS A 126 REMARK 465 LYS A 127 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 FE HEC A 201 N NO A 202 1.65 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 GLU A 6 CD GLU A 6 OE1 -0.072 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 ASP A 37 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 98 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 103 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES 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 526 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A 527 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH A 528 DISTANCE = 6.47 ANGSTROMS REMARK 525 HOH A 529 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH A 530 DISTANCE = 7.61 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 A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HEC A 201 NA 89.3 REMARK 620 3 HEC A 201 NB 86.9 89.3 REMARK 620 4 HEC A 201 NC 86.9 176.2 90.5 REMARK 620 5 HEC A 201 ND 87.6 90.0 174.5 89.9 REMARK 620 6 NO A 202 N 175.9 93.8 90.4 90.0 95.1 REMARK 620 7 NO A 202 O 168.5 99.0 85.2 84.8 100.4 7.4 REMARK 620 8 NO A 202 O 160.9 104.9 105.7 78.8 79.8 19.0 21.4 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEC A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO2 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO2 A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 212 DBREF 5NC0 A 1 127 UNP P00138 CYCP_ALCXX 1 127 SEQADV 5NC0 GLY A 16 UNP P00138 LEU 16 ENGINEERED MUTATION SEQRES 1 A 127 PCA PHE ALA LYS PRO GLU ASP ALA VAL LYS TYR ARG GLN SEQRES 2 A 127 SER ALA GLY THR LEU MET ALA SER HIS PHE GLY ARG MET SEQRES 3 A 127 THR PRO VAL VAL LYS GLY GLN ALA PRO TYR ASP ALA ALA SEQRES 4 A 127 GLN ILE LYS ALA ASN VAL GLU VAL LEU LYS THR LEU SER SEQRES 5 A 127 ALA LEU PRO TRP ALA ALA PHE GLY PRO GLY THR GLU GLY SEQRES 6 A 127 GLY ASP ALA ARG PRO GLU ILE TRP SER ASP ALA ALA SER SEQRES 7 A 127 PHE LYS GLN LYS GLN GLN ALA PHE GLN ASP ASN ILE VAL SEQRES 8 A 127 LYS LEU SER ALA ALA ALA ASP ALA GLY ASP LEU ASP LYS SEQRES 9 A 127 LEU ARG ALA ALA PHE GLY ASP VAL GLY ALA SER CYS LYS SEQRES 10 A 127 ALA CYS HIS ASP ALA TYR ARG LYS LYS LYS MODRES 5NC0 PCA A 1 GLN MODIFIED RESIDUE HET PCA A 1 8 HET HEC A 201 43 HET NO A 202 4 HET NO3 A 203 4 HET NO2 A 204 3 HET SO4 A 205 5 HET SO4 A 206 10 HET SO4 A 207 5 HET SO4 A 208 5 HET NO2 A 209 3 HET EDO A 210 4 HET EDO A 211 4 HET EDO A 212 4 HETNAM PCA PYROGLUTAMIC ACID HETNAM HEC HEME C HETNAM NO NITRIC OXIDE HETNAM NO3 NITRATE ION HETNAM NO2 NITRITE ION HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN NO NITROGEN MONOXIDE HETSYN EDO ETHYLENE GLYCOL FORMUL 1 PCA C5 H7 N O3 FORMUL 2 HEC C34 H34 FE N4 O4 FORMUL 3 NO N O FORMUL 4 NO3 N O3 1- FORMUL 5 NO2 2(N O2 1-) FORMUL 6 SO4 4(O4 S 2-) FORMUL 11 EDO 3(C2 H6 O2) FORMUL 14 HOH *230(H2 O) HELIX 1 AA1 LYS A 4 ARG A 25 1 22 HELIX 2 AA2 MET A 26 LYS A 31 1 6 HELIX 3 AA3 ASP A 37 ALA A 53 1 17 HELIX 4 AA4 LEU A 54 GLY A 60 5 7 HELIX 5 AA5 PRO A 70 ASP A 75 1 6 HELIX 6 AA6 ASP A 75 GLY A 100 1 26 HELIX 7 AA7 ASP A 101 ARG A 124 1 24 LINK C PCA A 1 N PHE A 2 1555 1555 1.34 LINK SG CYS A 116 CAB HEC A 201 1555 1555 1.85 LINK SG CYS A 119 CAC HEC A 201 1555 1555 1.85 LINK NE2 HIS A 120 FE HEC A 201 1555 1555 2.06 LINK FE HEC A 201 N B NO A 202 1555 1555 1.85 LINK FE HEC A 201 O A NO A 202 1555 1555 2.79 LINK FE HEC A 201 O B NO A 202 1555 1555 2.79 SITE 1 AC1 19 GLN A 13 GLY A 16 THR A 17 MET A 19 SITE 2 AC1 19 ALA A 20 TRP A 56 PHE A 59 ILE A 72 SITE 3 AC1 19 GLN A 83 PHE A 86 CYS A 116 CYS A 119 SITE 4 AC1 19 HIS A 120 ARG A 124 NO A 202 NO3 A 203 SITE 5 AC1 19 NO2 A 204 SO4 A 207 HOH A 333 SITE 1 AC2 5 MET A 19 PRO A 55 TRP A 56 HEC A 201 SITE 2 AC2 5 NO2 A 204 SITE 1 AC3 7 ARG A 12 GLN A 13 GLY A 65 GLY A 66 SITE 2 AC3 7 ASP A 67 ALA A 68 HEC A 201 SITE 1 AC4 5 ARG A 12 GLY A 16 PHE A 59 HEC A 201 SITE 2 AC4 5 NO A 202 SITE 1 AC5 4 ARG A 69 PRO A 70 GLU A 71 HOH A 528 SITE 1 AC6 11 PRO A 61 LYS A 92 ASP A 103 ARG A 106 SITE 2 AC6 11 ALA A 107 ASP A 111 HOH A 307 HOH A 334 SITE 3 AC6 11 HOH A 336 HOH A 441 HOH A 513 SITE 1 AC7 6 ASP A 67 ARG A 124 HEC A 201 HOH A 308 SITE 2 AC7 6 HOH A 321 HOH A 326 SITE 1 AC8 4 LYS A 117 HIS A 120 ARG A 124 HOH A 301 SITE 1 AC9 8 GLU A 6 GLY A 65 GLY A 66 GLN A 81 SITE 2 AC9 8 GLN A 84 ALA A 85 HOH A 323 HOH A 412 SITE 1 AD1 6 LYS A 49 THR A 50 HOH A 367 HOH A 385 SITE 2 AD1 6 HOH A 409 HOH A 487 SITE 1 AD2 3 LYS A 4 LYS A 82 HOH A 332 SITE 1 AD3 5 LYS A 49 ASP A 98 HOH A 304 HOH A 320 SITE 2 AD3 5 HOH A 330 CRYST1 52.430 52.430 183.250 90.00 90.00 120.00 P 65 2 2 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 0.019073 0.011012 0.000000 0.00000 SCALE2 0.000000 0.022024 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005457 0.00000 HETATM 1 N PCA A 1 -29.256 7.565 1.887 1.00 11.91 N ANISOU 1 N PCA A 1 1668 2157 698 1043 -383 -542 N HETATM 2 CA PCA A 1 -29.822 7.001 3.056 1.00 9.93 C ANISOU 2 CA PCA A 1 1572 1532 667 621 -561 -562 C HETATM 3 CB PCA A 1 -28.686 7.223 4.115 1.00 9.98 C ANISOU 3 CB PCA A 1 1652 1436 704 471 -611 -404 C HETATM 4 CG PCA A 1 -27.914 8.405 3.571 1.00 10.50 C ANISOU 4 CG PCA A 1 2156 1165 666 461 -612 -323 C HETATM 5 CD PCA A 1 -28.236 8.410 2.103 1.00 10.86 C ANISOU 5 CD PCA A 1 2061 1542 522 820 -416 -615 C HETATM 6 OE PCA A 1 -27.690 9.095 1.229 1.00 13.61 O ANISOU 6 OE PCA A 1 2253 2271 645 1033 -283 -340 O HETATM 7 C PCA A 1 -31.117 7.624 3.536 1.00 8.88 C ANISOU 7 C PCA A 1 1588 1405 380 437 -450 -361 C HETATM 8 O PCA A 1 -31.558 7.330 4.638 1.00 11.06 O ANISOU 8 O PCA A 1 2041 1620 539 476 -420 -98 O