HEADER METAL BINDING PROTEIN 28-OCT-10 2XVZ TITLE COBALT CHELATASE CBIK (PERIPLASMATIC) FROM DESULVOBRIO TITLE 2 VULGARIS HILDENBOROUGH (CO-CRYSTALLIZED WITH COBALT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHELATASE, PUTATIVE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 29-297; COMPND 5 SYNONYM: COBALT CHELATASE CBIK; COMPND 6 EC: 4.99.1.3; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS; SOURCE 3 ORGANISM_TAXID: 882; SOURCE 4 STRAIN: HILDENBOROUGH; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 GOLD (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET-28 KEYWDS METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.V.ROMAO,S.A.L.LOBO,M.A.CARRONDO,L.M.SARAIVA,P.M.MATIAS REVDAT 3 16-FEB-11 2XVZ 1 JRNL REVDAT 2 29-DEC-10 2XVZ 1 JRNL REVDAT 1 22-DEC-10 2XVZ 0 JRNL AUTH C.V.ROMAO,D.LADAKIS,S.A.L.LOBO,M.A.CARRONDO,A.A.BRINDLEY, JRNL AUTH 2 E.DEERY,P.M.MATIAS,R.W.PICKERSGILL,L.M.SARAIVA,M.J.WARREN JRNL TITL EVOLUTION IN A FAMILY OF CHELATASES FACILITATED BY THE JRNL TITL 2 INTRODUCTION OF ACTIVE SITE ASYMMETRY AND PROTEIN JRNL TITL 3 OLIGOMERIZATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 97 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21173279 JRNL DOI 10.1073/PNAS.1014298108 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0063 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 85.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 99.58 REMARK 3 NUMBER OF REFLECTIONS : 17055 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) : 0.17211 REMARK 3 R VALUE (WORKING SET) : 0.16960 REMARK 3 FREE R VALUE : 0.22022 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 917 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) : 2.400 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.462 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1205 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.23 REMARK 3 BIN R VALUE (WORKING SET) : 0.215 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.266 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1994 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 106 REMARK 3 SOLVENT ATOMS : 112 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.2 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.804 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.15 REMARK 3 B22 (A**2) : -0.15 REMARK 3 B33 (A**2) : 0.30 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.215 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.194 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.125 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.299 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2144 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2925 ; 1.989 ; 2.051 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 262 ; 5.792 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 85 ;35.638 ;23.059 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 322 ;16.795 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;18.993 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 312 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1609 ; 0.010 ; 0.021 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): 1313 ; 1.082 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2096 ; 2.070 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 831 ; 3.308 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 829 ; 5.220 ; 4.500 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 : MASK 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. THE SIDE-CHAINS OF THE AMINO ACID RESIDUES- GLU22, REMARK 3 GLU23, ARG25, LYS30, LYS51, MET52 WERE MODELLED WITH 0.5 OF REMARK 3 OCCUPANCY DUE TO THE LACK OF ELECTRON DENSITY PROBABLY REMARK 3 DUE TO DISORDER. THE FOLLOWING AMINO ACID RESIDUES WERE REMARK 3 MODELLED WITH DOUBLE CONFORMATION- ARG173, MET193. REMARK 4 REMARK 4 2XVZ COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-OCT-10. REMARK 100 THE PDBE ID CODE IS EBI-45921. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.42363 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18046 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.40 REMARK 200 RESOLUTION RANGE LOW (A) : 49.45 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 7.7 REMARK 200 R MERGE (I) : 0.067 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.6 REMARK 200 R MERGE FOR SHELL (I) : 0.411 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.90 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.7 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.7 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION SOLUTION: 100MM REMARK 280 TRIS-HCL PH8.5, 2M AMMONIUM SULFATE. THE DROP WAS REMARK 280 MADE BY ADDING 1UL OF PROTEIN PLUS 1.8UL OF CRYSTALLIZATION REMARK 280 SOLUTION AND 0.2UL OF 1M COBALT CHLORIDE. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 60.72050 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 60.72050 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 60.55000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 60.72050 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 60.72050 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 60.55000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 60.72050 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 60.72050 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 60.55000 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 60.72050 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 60.72050 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 60.55000 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 60.72050 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 60.72050 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 60.55000 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 60.72050 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 60.72050 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 60.55000 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 60.72050 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 60.72050 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 60.55000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 60.72050 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 60.72050 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 60.55000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 17730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 41440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -654.9 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 121.44100 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 121.44100 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 GLY A 1 REMARK 465 HIS A 2 REMARK 465 GLY A 3 REMARK 465 ALA A 4 REMARK 465 PRO A 5 REMARK 465 LYS A 6 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 LEU A 99 CA - CB - CG ANGL. DEV. = 17.2 DEGREES REMARK 500 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 3.2 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 LEU A 87 33.90 -99.79 REMARK 500 LYS A 110 13.68 58.95 REMARK 500 PRO A 120 -174.61 -68.54 REMARK 500 ASP A 175 118.95 -164.03 REMARK 500 REMARK 500 REMARK: NULL 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 HEM A1270 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 96 NE2 REMARK 620 2 HEM A1270 NA 89.8 REMARK 620 3 HEM A1270 NC 92.1 2.7 REMARK 620 4 HEM A1270 NB 87.3 76.7 78.1 REMARK 620 5 HIS A 96 NE2 169.8 80.3 78.1 88.1 REMARK 620 6 HEM A1270 ND 99.1 95.7 94.1 170.1 84.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A1271 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 154 NE2 REMARK 620 2 HIS A 216 NE2 98.7 REMARK 620 3 PER A1285 O1 150.2 107.5 REMARK 620 4 HOH A2106 O 74.2 82.6 122.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1283 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 164 OH REMARK 620 2 SO4 A1273 O2 122.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A1270 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A1271 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1272 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1273 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1274 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1275 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1276 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1277 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1278 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1279 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1280 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1281 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1282 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A1283 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PER A1285 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE ON THE DATABASE HAS A SIGNAL PEPTIDE, THE REMARK 999 SEQUENCE OF THE STRUCTURE PRESENTED STARTS ON RESIDUE 29 DBREF 2XVZ A 1 269 UNP Q72EC8 Q72EC8_DESVH 29 297 SEQRES 1 A 269 GLY HIS GLY ALA PRO LYS ALA GLN LYS THR GLY ILE LEU SEQRES 2 A 269 LEU VAL ALA PHE GLY THR SER VAL GLU GLU ALA ARG PRO SEQRES 3 A 269 ALA LEU ASP LYS MET GLY ASP ARG VAL ARG ALA ALA HIS SEQRES 4 A 269 PRO ASP ILE PRO VAL ARG TRP ALA TYR THR ALA LYS MET SEQRES 5 A 269 ILE ARG ALA LYS LEU ARG ALA GLU GLY ILE ALA ALA PRO SEQRES 6 A 269 SER PRO ALA GLU ALA LEU ALA GLY MET ALA GLU GLU GLY SEQRES 7 A 269 PHE THR HIS VAL ALA VAL GLN SER LEU HIS THR ILE PRO SEQRES 8 A 269 GLY GLU GLU PHE HIS GLY LEU LEU GLU THR ALA HIS ALA SEQRES 9 A 269 PHE GLN GLY LEU PRO LYS GLY LEU THR ARG VAL SER VAL SEQRES 10 A 269 GLY LEU PRO LEU ILE GLY THR THR ALA ASP ALA GLU ALA SEQRES 11 A 269 VAL ALA GLU ALA LEU VAL ALA SER LEU PRO ALA ASP ARG SEQRES 12 A 269 LYS PRO GLY GLU PRO VAL VAL PHE MET GLY HIS GLY THR SEQRES 13 A 269 PRO HIS PRO ALA ASP ILE CYS TYR PRO GLY LEU GLN TYR SEQRES 14 A 269 TYR LEU TRP ARG LEU ASP PRO ASP LEU LEU VAL GLY THR SEQRES 15 A 269 VAL GLU GLY SER PRO SER PHE ASP ASN VAL MET ALA GLU SEQRES 16 A 269 LEU ASP VAL ARG LYS ALA LYS ARG VAL TRP LEU MET PRO SEQRES 17 A 269 LEU MET ALA VAL ALA GLY ASP HIS ALA ARG ASN ASP MET SEQRES 18 A 269 ALA GLY ASP GLU ASP ASP SER TRP THR SER GLN LEU ALA SEQRES 19 A 269 ARG ARG GLY ILE GLU ALA LYS PRO VAL LEU HIS GLY THR SEQRES 20 A 269 ALA GLU SER ASP ALA VAL ALA ALA ILE TRP LEU ARG HIS SEQRES 21 A 269 LEU ASP ASP ALA LEU ALA ARG LEU ASN HET HEM A1270 43 HET CO A1271 1 HET SO4 A1272 5 HET SO4 A1273 5 HET SO4 A1274 5 HET GOL A1275 6 HET GOL A1276 6 HET GOL A1277 6 HET SO4 A1278 5 HET SO4 A1279 5 HET SO4 A1280 5 HET SO4 A1281 5 HET SO4 A1282 5 HET NA A1283 1 HET CL A1284 1 HET PER A1285 2 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CO COBALT (II) ION HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM PER PEROXIDE ION HETSYN HEM HEME HETSYN GOL GLYCERIN FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 CO CO 2+ FORMUL 4 SO4 8(O4 S 2-) FORMUL 5 GOL 3(C3 H8 O3) FORMUL 6 NA NA 1+ FORMUL 7 CL CL 1- FORMUL 8 PER O2 2- FORMUL 9 HOH *112(H2 O) HELIX 1 1 ARG A 25 HIS A 39 1 15 HELIX 2 2 ALA A 50 GLU A 60 1 11 HELIX 3 3 SER A 66 GLU A 77 1 12 HELIX 4 4 GLY A 92 GLN A 106 1 15 HELIX 5 5 THR A 124 LEU A 139 1 16 HELIX 6 6 HIS A 158 ASP A 161 5 4 HELIX 7 7 ILE A 162 ARG A 173 1 12 HELIX 8 8 SER A 188 ARG A 199 1 12 HELIX 9 9 GLY A 214 ASP A 220 1 7 HELIX 10 10 SER A 228 ARG A 236 1 9 HELIX 11 11 GLY A 246 GLU A 249 5 4 HELIX 12 12 SER A 250 ARG A 267 1 18 SHEET 1 AA 4 VAL A 44 TYR A 48 0 SHEET 2 AA 4 THR A 10 ALA A 16 1 O ILE A 12 N ARG A 45 SHEET 3 AA 4 HIS A 81 SER A 86 1 O HIS A 81 N GLY A 11 SHEET 4 AA 4 ARG A 114 GLY A 118 1 O ARG A 114 N VAL A 82 SHEET 1 AB 4 LEU A 178 THR A 182 0 SHEET 2 AB 4 VAL A 149 GLY A 153 1 O VAL A 149 N LEU A 179 SHEET 3 AB 4 ARG A 203 PRO A 208 1 O TRP A 205 N VAL A 150 SHEET 4 AB 4 GLU A 239 PRO A 242 1 O GLU A 239 N VAL A 204 LINK NE2 HIS A 96 FE HEM A1270 1555 1555 1.96 LINK FE HEM A1270 NE2 HIS A 96 1555 5555 2.26 LINK CO CO A1271 O2 PER A1285 1555 1555 2.62 LINK CO CO A1271 NE2 HIS A 216 1555 1555 2.04 LINK CO CO A1271 O1 PER A1285 1555 1555 1.80 LINK CO CO A1271 O HOH A2106 1555 1555 2.19 LINK CO CO A1271 NE2 HIS A 154 1555 1555 2.04 LINK O2 SO4 A1273 NA NA A1283 1555 1555 3.17 LINK NA NA A1283 OH TYR A 164 1555 1555 2.75 CISPEP 1 SER A 186 PRO A 187 0 1.29 SITE 1 AC1 7 PRO A 91 HIS A 96 LEU A 99 LEU A 119 SITE 2 AC1 7 PRO A 159 HOH A2040 HOH A2105 SITE 1 AC2 5 HIS A 154 GLU A 184 HIS A 216 PER A1285 SITE 2 AC2 5 HOH A2106 SITE 1 AC3 8 GLY A 92 GLU A 93 GLU A 94 THR A 156 SITE 2 AC3 8 HIS A 158 HOH A2037 HOH A2055 HOH A2107 SITE 1 AC4 8 PHE A 17 LEU A 87 HIS A 88 THR A 89 SITE 2 AC4 8 MET A 210 ALA A 211 NA A1283 HOH A2108 SITE 1 AC5 5 ARG A 114 VAL A 115 SER A 116 VAL A 117 SITE 2 AC5 5 ARG A 267 SITE 1 AC6 5 LEU A 174 ASP A 175 ASP A 197 ARG A 236 SITE 2 AC6 5 HOH A2065 SITE 1 AC7 3 TRP A 172 PRO A 176 ARG A 199 SITE 1 AC8 4 THR A 49 LYS A 51 MET A 52 GLU A 94 SITE 1 AC9 3 PRO A 140 ALA A 141 HOH A2109 SITE 1 BC1 3 SER A 250 ASP A 251 ALA A 252 SITE 1 BC2 6 THR A 19 SER A 20 VAL A 21 ASP A 215 SITE 2 BC2 6 SO4 A1281 HOH A2110 SITE 1 BC3 7 GLY A 214 ASP A 215 HIS A 216 SO4 A1280 SITE 2 BC3 7 HOH A2106 HOH A2110 HOH A2111 SITE 1 BC4 4 PRO A 43 VAL A 44 ARG A 45 HOH A2112 SITE 1 BC5 4 GLY A 153 HIS A 154 TYR A 164 SO4 A1273 SITE 1 BC6 4 HIS A 154 GLU A 184 HIS A 216 CO A1271 CRYST1 121.441 121.441 121.100 90.00 90.00 90.00 I 4 2 2 16 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 0.008234 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008234 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008258 0.00000