HEADER ELECTRON TRANSPORT 28-MAR-17 5XDH TITLE HIS/DOPA LIGATED CYTOCHROME C FROM AN ANAMMOX ORGANISM KSU-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE CYTOCHROME C; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANDIDATUS JETTENIA CAENI; SOURCE 3 ORGANISM_TAXID: 247490; SOURCE 4 STRAIN: KSU-1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS CYTOCHROME C, ET PROTEIN, DOPA LIGAND, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR D.HIRA,R.KITAMURA,T.NAKAMURA,Y.YAMAGATA,K.FURUKAWA,T.FUJII REVDAT 4 02-OCT-19 5XDH 1 COMPND HET HETNAM HETSYN REVDAT 4 2 1 FORMUL LINK ATOM REVDAT 3 18-APR-18 5XDH 1 JRNL REVDAT 2 11-APR-18 5XDH 1 JRNL REVDAT 1 28-MAR-18 5XDH 0 JRNL AUTH D.HIRA,R.KITAMURA,T.NAKAMURA,Y.YAMAGATA,K.FURUKAWA,T.FUJII JRNL TITL ANAMMOX ORGANISM KSU-1 EXPRESSES A NOVEL HIS/DOPA LIGATED JRNL TITL 2 CYTOCHROME C. JRNL REF J. MOL. BIOL. V. 430 1189 2018 JRNL REFN ESSN 1089-8638 JRNL PMID 29481839 JRNL DOI 10.1016/J.JMB.2018.02.017 REMARK 2 REMARK 2 RESOLUTION. 1.32 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) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 79049 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) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 4109 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) : 1.32 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5598 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.1850 REMARK 3 BIN FREE R VALUE SET COUNT : 260 REMARK 3 BIN FREE R VALUE : 0.2030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2610 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 195 REMARK 3 SOLVENT ATOMS : 512 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.66000 REMARK 3 B22 (A**2) : 0.23000 REMARK 3 B33 (A**2) : 0.59000 REMARK 3 B12 (A**2) : -0.17000 REMARK 3 B13 (A**2) : -0.36000 REMARK 3 B23 (A**2) : -0.09000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.049 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.050 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.029 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.387 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3093 ; 0.015 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2732 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4251 ; 1.822 ; 2.082 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6416 ; 1.260 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 400 ; 5.324 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;32.368 ;26.842 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 529 ;13.011 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;22.044 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 431 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3568 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 596 ; 0.015 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 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): 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 101 REMARK 3 ORIGIN FOR THE GROUP (A): 7.8839 15.2814 -5.5503 REMARK 3 T TENSOR REMARK 3 T11: 0.0340 T22: 0.0332 REMARK 3 T33: 0.0247 T12: 0.0032 REMARK 3 T13: 0.0092 T23: 0.0023 REMARK 3 L TENSOR REMARK 3 L11: 0.6893 L22: 0.2410 REMARK 3 L33: 0.0331 L12: 0.1190 REMARK 3 L13: -0.0390 L23: 0.0695 REMARK 3 S TENSOR REMARK 3 S11: -0.0200 S12: 0.0063 S13: 0.0623 REMARK 3 S21: -0.0092 S22: 0.0190 S23: 0.0083 REMARK 3 S31: 0.0104 S32: 0.0018 S33: 0.0010 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 101 REMARK 3 ORIGIN FOR THE GROUP (A): 10.2112 -1.3199 15.1444 REMARK 3 T TENSOR REMARK 3 T11: 0.0339 T22: 0.0428 REMARK 3 T33: 0.0038 T12: 0.0021 REMARK 3 T13: 0.0054 T23: 0.0029 REMARK 3 L TENSOR REMARK 3 L11: 0.3253 L22: 0.3229 REMARK 3 L33: 0.8031 L12: 0.1053 REMARK 3 L13: 0.2685 L23: 0.2485 REMARK 3 S TENSOR REMARK 3 S11: 0.0547 S12: -0.0169 S13: -0.0116 REMARK 3 S21: -0.0235 S22: -0.0143 S23: -0.0285 REMARK 3 S31: 0.0047 S32: 0.0152 S33: -0.0404 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 101 REMARK 3 ORIGIN FOR THE GROUP (A): -11.5698 3.1399 -13.3015 REMARK 3 T TENSOR REMARK 3 T11: 0.0285 T22: 0.0336 REMARK 3 T33: 0.0287 T12: 0.0098 REMARK 3 T13: -0.0061 T23: 0.0079 REMARK 3 L TENSOR REMARK 3 L11: 0.9982 L22: 0.1155 REMARK 3 L33: 0.3179 L12: -0.2120 REMARK 3 L13: 0.3258 L23: 0.0306 REMARK 3 S TENSOR REMARK 3 S11: 0.0066 S12: 0.0468 S13: -0.0651 REMARK 3 S21: 0.0228 S22: 0.0145 S23: 0.0186 REMARK 3 S31: 0.0144 S32: 0.0132 S33: -0.0212 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 101 REMARK 3 ORIGIN FOR THE GROUP (A): -5.6552 -16.3710 4.4720 REMARK 3 T TENSOR REMARK 3 T11: 0.0247 T22: 0.0228 REMARK 3 T33: 0.0301 T12: 0.0063 REMARK 3 T13: 0.0033 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 0.3271 L22: 0.4980 REMARK 3 L33: 0.3550 L12: 0.2998 REMARK 3 L13: 0.0974 L23: 0.2626 REMARK 3 S TENSOR REMARK 3 S11: -0.0005 S12: -0.0135 S13: -0.0055 REMARK 3 S21: 0.0036 S22: -0.0496 S23: -0.0072 REMARK 3 S31: -0.0216 S32: -0.0107 S33: 0.0500 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 5XDH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-APR-17. REMARK 100 THE DEPOSITION ID IS D_1300003327. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-16; 14-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SPRING-8; SPRING-8 REMARK 200 BEAMLINE : BL44XU; BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9; 1.7 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE; RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000, HKL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 83160 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.320 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.30400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.2M AMMONIUM SULFATE, 200MM POTASSIUM REMARK 280 SODIUM TARTRATE, 100MM SODIUM ACETATE, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z 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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 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 C 86 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 O ASP D 65 O HOH D 201 2.09 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 MET A 47 CG - SD - CE ANGL. DEV. = -12.3 DEGREES REMARK 500 LEU A 63 CA - CB - CG ANGL. DEV. = 14.6 DEGREES REMARK 500 MET B 51 CG - SD - CE ANGL. DEV. = -17.8 DEGREES REMARK 500 ARG D 42 NE - CZ - NH1 ANGL. DEV. = 3.8 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 THR A 10 12.80 -143.11 REMARK 500 THR B 10 -52.89 -123.36 REMARK 500 THR C 10 -60.56 -108.57 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 353 DISTANCE = 6.71 ANGSTROMS REMARK 525 HOH B 319 DISTANCE = 6.36 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 101 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 15 NE2 REMARK 620 2 HEC A 101 NA 90.9 REMARK 620 3 HEC A 101 NB 88.4 89.8 REMARK 620 4 HEC A 101 NC 88.1 179.0 89.9 REMARK 620 5 HEC A 101 ND 90.9 90.6 179.2 89.8 REMARK 620 6 DAH A 60 OE2 175.2 89.5 86.8 91.5 93.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC B 101 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 15 NE2 REMARK 620 2 HEC B 101 NA 89.6 REMARK 620 3 HEC B 101 NB 89.1 90.4 REMARK 620 4 HEC B 101 NC 89.6 179.0 89.1 REMARK 620 5 HEC B 101 ND 90.6 90.0 179.4 90.4 REMARK 620 6 DAH B 60 OE2 175.4 90.9 86.4 89.9 94.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC C 101 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 15 NE2 REMARK 620 2 HEC C 101 NA 90.8 REMARK 620 3 HEC C 101 NB 88.4 90.6 REMARK 620 4 HEC C 101 NC 88.3 179.0 89.2 REMARK 620 5 HEC C 101 ND 91.5 89.3 179.8 90.9 REMARK 620 6 DAH C 60 OE2 174.2 91.0 86.1 89.9 94.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC D 101 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 15 NE2 REMARK 620 2 HEC D 101 NA 89.8 REMARK 620 3 HEC D 101 NB 88.2 89.3 REMARK 620 4 HEC D 101 NC 89.4 179.1 90.3 REMARK 620 5 HEC D 101 ND 90.9 90.4 179.1 90.0 REMARK 620 6 DAH D 60 OE2 175.0 90.1 86.8 90.7 94.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Ligand residues DAH A 60 REMARK 800 through CYS A 14 bound to ASN A 59 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Ligand residues DAH B 60 REMARK 800 through CYS B 11 bound to ASN B 59 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Ligand residues DAH C 60 REMARK 800 through CYS C 11 bound to ASN C 59 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Ligand residues DAH D 60 REMARK 800 through CYS D 11 bound to ASN D 59 DBREF 5XDH A 1 86 UNP I3IL56 I3IL56_9BACT 30 115 DBREF 5XDH B 1 86 UNP I3IL56 I3IL56_9BACT 30 115 DBREF 5XDH C 1 86 UNP I3IL56 I3IL56_9BACT 30 115 DBREF 5XDH D 1 86 UNP I3IL56 I3IL56_9BACT 30 115 SEQADV 5XDH DAH A 60 UNP I3IL56 TYR 89 ENGINEERED MUTATION SEQADV 5XDH DAH B 60 UNP I3IL56 TYR 89 ENGINEERED MUTATION SEQADV 5XDH DAH C 60 UNP I3IL56 TYR 89 ENGINEERED MUTATION SEQADV 5XDH DAH D 60 UNP I3IL56 TYR 89 ENGINEERED MUTATION SEQRES 1 A 86 GLY ASP ILE GLN LYS THR TYR LYS ASP THR CYS GLU LEU SEQRES 2 A 86 CYS HIS GLY ALA ASP GLY LYS GLY SER GLU ALA GLY LYS SEQRES 3 A 86 GLN PHE GLY VAL PRO ASP PHE THR SER PRO ASP TYR GLN SEQRES 4 A 86 LYS SER ARG THR ASP ALA GLN MET LYS GLU SER MET THR SEQRES 5 A 86 ASN GLY THR LYS ASN PRO ASN DAH VAL LYS LEU SER ASP SEQRES 6 A 86 LEU GLY VAL ASP LEU ALA ASP LEU ASP PRO LEU VAL GLN SEQRES 7 A 86 LEU VAL ARG GLY PHE ASN GLY LYS SEQRES 1 B 86 GLY ASP ILE GLN LYS THR TYR LYS ASP THR CYS GLU LEU SEQRES 2 B 86 CYS HIS GLY ALA ASP GLY LYS GLY SER GLU ALA GLY LYS SEQRES 3 B 86 GLN PHE GLY VAL PRO ASP PHE THR SER PRO ASP TYR GLN SEQRES 4 B 86 LYS SER ARG THR ASP ALA GLN MET LYS GLU SER MET THR SEQRES 5 B 86 ASN GLY THR LYS ASN PRO ASN DAH VAL LYS LEU SER ASP SEQRES 6 B 86 LEU GLY VAL ASP LEU ALA ASP LEU ASP PRO LEU VAL GLN SEQRES 7 B 86 LEU VAL ARG GLY PHE ASN GLY LYS SEQRES 1 C 86 GLY ASP ILE GLN LYS THR TYR LYS ASP THR CYS GLU LEU SEQRES 2 C 86 CYS HIS GLY ALA ASP GLY LYS GLY SER GLU ALA GLY LYS SEQRES 3 C 86 GLN PHE GLY VAL PRO ASP PHE THR SER PRO ASP TYR GLN SEQRES 4 C 86 LYS SER ARG THR ASP ALA GLN MET LYS GLU SER MET THR SEQRES 5 C 86 ASN GLY THR LYS ASN PRO ASN DAH VAL LYS LEU SER ASP SEQRES 6 C 86 LEU GLY VAL ASP LEU ALA ASP LEU ASP PRO LEU VAL GLN SEQRES 7 C 86 LEU VAL ARG GLY PHE ASN GLY LYS SEQRES 1 D 86 GLY ASP ILE GLN LYS THR TYR LYS ASP THR CYS GLU LEU SEQRES 2 D 86 CYS HIS GLY ALA ASP GLY LYS GLY SER GLU ALA GLY LYS SEQRES 3 D 86 GLN PHE GLY VAL PRO ASP PHE THR SER PRO ASP TYR GLN SEQRES 4 D 86 LYS SER ARG THR ASP ALA GLN MET LYS GLU SER MET THR SEQRES 5 D 86 ASN GLY THR LYS ASN PRO ASN DAH VAL LYS LEU SER ASP SEQRES 6 D 86 LEU GLY VAL ASP LEU ALA ASP LEU ASP PRO LEU VAL GLN SEQRES 7 D 86 LEU VAL ARG GLY PHE ASN GLY LYS HET DAH A 60 13 HET DAH B 60 13 HET DAH C 60 13 HET DAH D 60 13 HET HEC A 101 43 HET ACT A 102 4 HET ACT A 103 4 HET SO4 A 104 5 HET HEC B 101 43 HET SO4 B 102 5 HET HEC C 101 43 HET HEC D 101 43 HET SO4 D 102 5 HETNAM DAH 3,4-DIHYDROXYPHENYLALANINE HETNAM HEC HEME C HETNAM ACT ACETATE ION HETNAM SO4 SULFATE ION HETSYN DAH L-DOPA FORMUL 1 DAH 4(C9 H11 N O4) FORMUL 5 HEC 4(C34 H34 FE N4 O4) FORMUL 6 ACT 2(C2 H3 O2 1-) FORMUL 8 SO4 3(O4 S 2-) FORMUL 14 HOH *512(H2 O) HELIX 1 AA1 GLY A 1 CYS A 11 1 11 HELIX 2 AA2 CYS A 11 GLY A 16 1 6 HELIX 3 AA3 SER A 22 GLY A 29 1 8 HELIX 4 AA4 SER A 35 SER A 41 1 7 HELIX 5 AA5 THR A 43 GLY A 54 1 12 HELIX 6 AA6 ASP A 69 ALA A 71 5 3 HELIX 7 AA7 ASP A 72 GLY A 82 1 11 HELIX 8 AA8 ASP B 2 CYS B 11 1 10 HELIX 9 AA9 CYS B 11 GLY B 16 1 6 HELIX 10 AB1 SER B 22 GLY B 29 1 8 HELIX 11 AB2 SER B 35 ARG B 42 1 8 HELIX 12 AB3 THR B 43 GLY B 54 1 12 HELIX 13 AB4 LYS B 62 GLY B 67 5 6 HELIX 14 AB5 ASP B 69 ALA B 71 5 3 HELIX 15 AB6 ASP B 72 PHE B 83 1 12 HELIX 16 AB7 ASP C 2 CYS C 11 1 10 HELIX 17 AB8 CYS C 11 GLY C 16 1 6 HELIX 18 AB9 SER C 22 GLY C 29 1 8 HELIX 19 AC1 SER C 35 SER C 41 1 7 HELIX 20 AC2 THR C 43 GLY C 54 1 12 HELIX 21 AC3 LYS C 62 GLY C 67 5 6 HELIX 22 AC4 ASP C 69 ALA C 71 5 3 HELIX 23 AC5 ASP C 72 PHE C 83 1 12 HELIX 24 AC6 ASP D 2 CYS D 11 1 10 HELIX 25 AC7 CYS D 11 GLY D 16 1 6 HELIX 26 AC8 SER D 22 GLY D 29 1 8 HELIX 27 AC9 SER D 35 SER D 41 1 7 HELIX 28 AD1 THR D 43 GLY D 54 1 12 HELIX 29 AD2 LYS D 62 GLY D 67 5 6 HELIX 30 AD3 ASP D 69 ALA D 71 5 3 HELIX 31 AD4 ASP D 72 GLY D 82 1 11 LINK SG CYS A 11 CAB HEC A 101 1555 1555 1.86 LINK SG CYS A 14 CAC HEC A 101 1555 1555 1.91 LINK NE2 HIS A 15 FE HEC A 101 1555 1555 2.03 LINK C ASN A 59 N DAH A 60 1555 1555 1.32 LINK C DAH A 60 N VAL A 61 1555 1555 1.32 LINK OE2 DAH A 60 FE HEC A 101 1555 1555 1.96 LINK SG CYS B 11 CAB HEC B 101 1555 1555 1.88 LINK SG CYS B 14 CAC HEC B 101 1555 1555 1.90 LINK NE2 HIS B 15 FE HEC B 101 1555 1555 2.02 LINK C ASN B 59 N DAH B 60 1555 1555 1.33 LINK C DAH B 60 N VAL B 61 1555 1555 1.32 LINK OE2 DAH B 60 FE HEC B 101 1555 1555 1.96 LINK SG CYS C 11 CAB HEC C 101 1555 1555 1.87 LINK SG CYS C 14 CAC HEC C 101 1555 1555 1.90 LINK NE2 HIS C 15 FE HEC C 101 1555 1555 2.03 LINK C ASN C 59 N DAH C 60 1555 1555 1.34 LINK C DAH C 60 N VAL C 61 1555 1555 1.32 LINK OE2 DAH C 60 FE HEC C 101 1555 1555 1.97 LINK SG CYS D 11 CAB HEC D 101 1555 1555 1.87 LINK SG CYS D 14 CAC HEC D 101 1555 1555 1.90 LINK NE2 HIS D 15 FE HEC D 101 1555 1555 2.02 LINK C ASN D 59 N DAH D 60 1555 1555 1.33 LINK C DAH D 60 N VAL D 61 1555 1555 1.32 LINK OE2 DAH D 60 FE HEC D 101 1555 1555 1.97 LINK CB DAH A 60 O1D HEC A 101 1555 1555 1.61 LINK CB DAH B 60 O1D HEC B 101 1555 1555 1.65 LINK CB DAH C 60 O1D HEC C 101 1555 1555 1.60 LINK CB DAH D 60 O1D HEC D 101 1555 1555 1.64 SITE 1 AC1 5 ARG A 81 HOH A 202 GLN D 39 ARG D 81 SITE 2 AC1 5 HOH D 276 SITE 1 AC2 8 ASP A 44 ALA A 45 LYS A 48 HOH A 209 SITE 2 AC2 8 HOH A 219 HOH A 221 HOH D 239 HOH D 303 SITE 1 AC3 5 GLY A 1 ASP A 2 ILE A 3 GLN A 4 SITE 2 AC3 5 HOH A 222 SITE 1 AC4 4 THR B 55 LYS B 56 HOH B 209 HOH B 275 SITE 1 AC5 6 GLY D 1 ASP D 2 ILE D 3 GLN D 4 SITE 2 AC5 6 HOH D 230 HOH D 258 SITE 1 AC6 33 TYR A 7 THR A 10 GLU A 12 LEU A 13 SITE 2 AC6 33 HIS A 15 GLY A 16 GLY A 21 SER A 22 SITE 3 AC6 33 GLY A 25 PHE A 28 GLY A 29 VAL A 30 SITE 4 AC6 33 PHE A 33 TYR A 38 ARG A 42 MET A 47 SITE 5 AC6 33 SER A 50 MET A 51 THR A 55 ASN A 57 SITE 6 AC6 33 PRO A 58 ASN A 59 LYS A 62 LEU A 63 SITE 7 AC6 33 ASP A 65 LEU A 66 HOH A 206 HOH A 228 SITE 8 AC6 33 HOH A 235 HOH A 252 HOH A 263 GLN C 27 SITE 9 AC6 33 PHE C 28 SITE 1 AC7 32 TYR B 7 THR B 10 GLU B 12 LEU B 13 SITE 2 AC7 32 HIS B 15 GLY B 16 GLY B 21 SER B 22 SITE 3 AC7 32 GLY B 25 PHE B 28 GLY B 29 VAL B 30 SITE 4 AC7 32 PHE B 33 TYR B 38 ARG B 42 MET B 47 SITE 5 AC7 32 SER B 50 MET B 51 THR B 55 ASN B 57 SITE 6 AC7 32 PRO B 58 ASN B 59 LYS B 62 LEU B 63 SITE 7 AC7 32 ASP B 65 HOH B 206 HOH B 238 HOH B 249 SITE 8 AC7 32 HOH B 269 HOH B 282 GLN D 27 PHE D 28 SITE 1 AC8 31 GLN A 27 PHE A 28 TYR C 7 THR C 10 SITE 2 AC8 31 GLU C 12 LEU C 13 HIS C 15 GLY C 16 SITE 3 AC8 31 GLY C 21 SER C 22 GLY C 25 PHE C 28 SITE 4 AC8 31 GLY C 29 VAL C 30 PHE C 33 TYR C 38 SITE 5 AC8 31 ARG C 42 MET C 47 SER C 50 MET C 51 SITE 6 AC8 31 THR C 55 ASN C 57 PRO C 58 ASN C 59 SITE 7 AC8 31 LYS C 62 LEU C 63 ASP C 65 HOH C 218 SITE 8 AC8 31 HOH C 229 HOH C 249 HOH C 277 SITE 1 AC9 33 PHE B 28 TYR D 7 THR D 10 GLU D 12 SITE 2 AC9 33 LEU D 13 HIS D 15 GLY D 16 GLY D 21 SITE 3 AC9 33 SER D 22 GLY D 25 PHE D 28 GLY D 29 SITE 4 AC9 33 VAL D 30 PHE D 33 TYR D 38 ARG D 42 SITE 5 AC9 33 MET D 47 SER D 50 MET D 51 THR D 55 SITE 6 AC9 33 ASN D 57 PRO D 58 ASN D 59 LYS D 62 SITE 7 AC9 33 LEU D 63 ASP D 65 LEU D 66 VAL D 68 SITE 8 AC9 33 HOH D 211 HOH D 213 HOH D 237 HOH D 251 SITE 9 AC9 33 HOH D 267 CRYST1 42.794 47.687 48.993 96.46 99.01 102.13 P 1 4 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 0.023368 0.005023 0.004513 0.00000 SCALE2 0.000000 0.021449 0.003267 0.00000 SCALE3 0.000000 0.000000 0.020904 0.00000