HEADER PROTEIN BINDING 01-MAR-13 4JGI TITLE 1.5 ANGSTROM CRYSTAL STRUCTURE OF A NOVEL COBALAMIN-BINDING PROTEIN TITLE 2 FROM DESULFITOBACTERIUM HAFNIENSE DCB-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFITOBACTERIUM HAFNIENSE; SOURCE 3 ORGANISM_TAXID: 49338; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ROSSMANN FOLD, COBALAMIN BINDING, COBALAMIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR H.SJUTS,M.S.DUNSTAN,K.FISHER,D.LEYS REVDAT 3 28-FEB-24 4JGI 1 REMARK SEQADV LINK REVDAT 2 15-NOV-17 4JGI 1 REMARK REVDAT 1 07-AUG-13 4JGI 0 JRNL AUTH H.SJUTS,M.S.DUNSTAN,K.FISHER,D.LEYS JRNL TITL STRUCTURE OF THE COBALAMIN-BINDING PROTEIN OF A PUTATIVE JRNL TITL 2 O-DEMETHYLASE FROM DESULFITOBACTERIUM HAFNIENSE DCB-2. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 69 1609 2013 JRNL REFN ISSN 0907-4449 JRNL PMID 23897483 JRNL DOI 10.1107/S0907444913011323 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 75677 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) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3997 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5479 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.38 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 314 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3065 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 182 REMARK 3 SOLVENT ATOMS : 421 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.08000 REMARK 3 B12 (A**2) : 0.03000 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): 0.066 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.065 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.043 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.603 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3295 ; 0.021 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3235 ; 0.001 ; 0.019 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4484 ; 2.140 ; 1.998 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7418 ; 1.018 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 407 ; 6.091 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;40.287 ;26.269 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 555 ;13.485 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;15.345 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 526 ; 0.140 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3933 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 669 ; 0.001 ; 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): 6530 ; 7.088 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 102 ;22.138 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6801 ;12.053 ; 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 : 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4JGI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000078016. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 XDS REMARK 200 DATA SCALING SOFTWARE : XIA2 XDS SCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75677 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 32.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MMT BUFFER, 25 % W/V PEG 1500, REMARK 280 PH 8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.56000 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 61.12000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 34.99500 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -60.61312 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 30.56000 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 SER A 82 REMARK 465 GLY A 83 REMARK 465 ASP A 84 REMARK 465 ALA A 85 REMARK 465 LEU A 86 REMARK 465 GLU A 87 REMARK 465 SER B 82 REMARK 465 GLY B 83 REMARK 465 ASP B 84 REMARK 465 ALA B 85 REMARK 465 LEU B 86 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 VAL A 1 CG1 CG2 REMARK 470 ILE A 2 CG1 CG2 CD1 REMARK 470 LEU A 81 CG CD1 CD2 REMARK 470 LYS A 88 CG CD CE NZ REMARK 470 GLU B 87 CG CD OE1 OE2 REMARK 470 LYS B 88 CG CD CE NZ 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 GLU B 87 O HOH B 483 2.15 REMARK 500 O SER A 196 O HOH A 597 2.15 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 98 CD GLU A 98 OE1 -0.067 REMARK 500 GLU B 16 CD GLU B 16 OE2 0.068 REMARK 500 GLU B 98 CG GLU B 98 CD 0.098 REMARK 500 GLU B 98 CD GLU B 98 OE1 0.179 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 27 CG - SD - CE ANGL. DEV. = 12.2 DEGREES REMARK 500 MET A 46 CG - SD - CE ANGL. DEV. = -14.8 DEGREES REMARK 500 ASP A 126 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 LYS A 165 CD - CE - NZ ANGL. DEV. = 18.9 DEGREES REMARK 500 GLU B 98 CG - CD - OE1 ANGL. DEV. = 15.3 DEGREES REMARK 500 ASP B 126 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 134 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG B 189 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 208 NE - CZ - NH1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG B 208 NE - CZ - NH2 ANGL. DEV. = -4.0 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 ILE A 2 -77.73 -61.28 REMARK 500 VAL A 149 -44.77 -133.75 REMARK 500 ALA B 32 -51.41 104.79 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 COB A 301 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 102 NE2 REMARK 620 2 COB A 301 N21 96.6 REMARK 620 3 COB A 301 N22 93.2 90.3 REMARK 620 4 COB A 301 N23 80.3 173.6 95.4 REMARK 620 5 COB A 301 N24 95.7 82.6 169.2 92.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 COB B 301 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 102 NE2 REMARK 620 2 COB B 301 N21 97.5 REMARK 620 3 COB B 301 N22 91.3 89.9 REMARK 620 4 COB B 301 N23 81.3 173.4 96.6 REMARK 620 5 COB B 301 N24 99.5 82.5 167.6 91.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE COB A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE COB B 301 DBREF 4JGI A 11 211 UNP Q8RPG0 Q8RPG0_DESHA 1 201 DBREF 4JGI B 11 211 UNP Q8RPG0 Q8RPG0_DESHA 1 201 SEQADV 4JGI VAL A 1 UNP Q8RPG0 EXPRESSION TAG SEQADV 4JGI ILE A 2 UNP Q8RPG0 EXPRESSION TAG SEQADV 4JGI ASP A 3 UNP Q8RPG0 EXPRESSION TAG SEQADV 4JGI LEU A 4 UNP Q8RPG0 EXPRESSION TAG SEQADV 4JGI ASN A 5 UNP Q8RPG0 EXPRESSION TAG SEQADV 4JGI ALA A 6 UNP Q8RPG0 EXPRESSION TAG SEQADV 4JGI SER A 7 UNP Q8RPG0 EXPRESSION TAG SEQADV 4JGI ALA A 8 UNP Q8RPG0 EXPRESSION TAG SEQADV 4JGI GLN A 9 UNP Q8RPG0 EXPRESSION TAG SEQADV 4JGI ALA A 10 UNP Q8RPG0 EXPRESSION TAG SEQADV 4JGI VAL B 1 UNP Q8RPG0 EXPRESSION TAG SEQADV 4JGI ILE B 2 UNP Q8RPG0 EXPRESSION TAG SEQADV 4JGI ASP B 3 UNP Q8RPG0 EXPRESSION TAG SEQADV 4JGI LEU B 4 UNP Q8RPG0 EXPRESSION TAG SEQADV 4JGI ASN B 5 UNP Q8RPG0 EXPRESSION TAG SEQADV 4JGI ALA B 6 UNP Q8RPG0 EXPRESSION TAG SEQADV 4JGI SER B 7 UNP Q8RPG0 EXPRESSION TAG SEQADV 4JGI ALA B 8 UNP Q8RPG0 EXPRESSION TAG SEQADV 4JGI GLN B 9 UNP Q8RPG0 EXPRESSION TAG SEQADV 4JGI ALA B 10 UNP Q8RPG0 EXPRESSION TAG SEQRES 1 A 211 VAL ILE ASP LEU ASN ALA SER ALA GLN ALA MET SER ASP SEQRES 2 A 211 LEU ASP GLU GLY ALA ILE ASN GLU VAL VAL ASP LYS VAL SEQRES 3 A 211 MET ALA LYS ALA ASP ALA ASP ALA ALA GLN GLU LEU ILE SEQRES 4 A 211 LYS ALA PHE GLN GLN GLY MET THR LYS VAL GLY GLU ARG SEQRES 5 A 211 PHE ASP SER GLY GLU TYR PHE ILE GLY ASP LEU ILE PHE SEQRES 6 A 211 ALA GLY GLU ILE LEU GLN ALA ALA MET ASP LYS LEU LYS SEQRES 7 A 211 PRO ALA LEU SER GLY ASP ALA LEU GLU LYS ARG ALA LYS SEQRES 8 A 211 ILE VAL LEU ALA THR VAL GLU GLY ASP LEU HIS ASP ILE SEQRES 9 A 211 GLY LYS ASN ILE PHE ARG THR MET ALA GLU ALA SER GLY SEQRES 10 A 211 PHE GLU VAL PHE ASP LEU GLY ILE ASP VAL PRO VAL LYS SEQRES 11 A 211 ILE ILE VAL ASP LYS VAL LYS GLU VAL ASN PRO GLU ILE SEQRES 12 A 211 VAL GLY LEU SER GLY VAL LEU THR LEU ALA LEU ASP SER SEQRES 13 A 211 MET ARG GLU THR VAL ASP ALA LEU LYS ALA GLU GLY LEU SEQRES 14 A 211 ARG ASN ASP LEU LYS VAL ILE ILE GLY GLY VAL PRO VAL SEQRES 15 A 211 ASN GLU ASN VAL CYS GLN ARG VAL GLY ALA ASP ASP PHE SEQRES 16 A 211 SER THR ASN ALA ALA ASP GLY VAL LYS ILE CYS GLN ARG SEQRES 17 A 211 TRP VAL GLY SEQRES 1 B 211 VAL ILE ASP LEU ASN ALA SER ALA GLN ALA MET SER ASP SEQRES 2 B 211 LEU ASP GLU GLY ALA ILE ASN GLU VAL VAL ASP LYS VAL SEQRES 3 B 211 MET ALA LYS ALA ASP ALA ASP ALA ALA GLN GLU LEU ILE SEQRES 4 B 211 LYS ALA PHE GLN GLN GLY MET THR LYS VAL GLY GLU ARG SEQRES 5 B 211 PHE ASP SER GLY GLU TYR PHE ILE GLY ASP LEU ILE PHE SEQRES 6 B 211 ALA GLY GLU ILE LEU GLN ALA ALA MET ASP LYS LEU LYS SEQRES 7 B 211 PRO ALA LEU SER GLY ASP ALA LEU GLU LYS ARG ALA LYS SEQRES 8 B 211 ILE VAL LEU ALA THR VAL GLU GLY ASP LEU HIS ASP ILE SEQRES 9 B 211 GLY LYS ASN ILE PHE ARG THR MET ALA GLU ALA SER GLY SEQRES 10 B 211 PHE GLU VAL PHE ASP LEU GLY ILE ASP VAL PRO VAL LYS SEQRES 11 B 211 ILE ILE VAL ASP LYS VAL LYS GLU VAL ASN PRO GLU ILE SEQRES 12 B 211 VAL GLY LEU SER GLY VAL LEU THR LEU ALA LEU ASP SER SEQRES 13 B 211 MET ARG GLU THR VAL ASP ALA LEU LYS ALA GLU GLY LEU SEQRES 14 B 211 ARG ASN ASP LEU LYS VAL ILE ILE GLY GLY VAL PRO VAL SEQRES 15 B 211 ASN GLU ASN VAL CYS GLN ARG VAL GLY ALA ASP ASP PHE SEQRES 16 B 211 SER THR ASN ALA ALA ASP GLY VAL LYS ILE CYS GLN ARG SEQRES 17 B 211 TRP VAL GLY HET COB A 301 91 HET COB B 301 91 HETNAM COB CO-METHYLCOBALAMIN FORMUL 3 COB 2(C63 H91 CO N13 O14 P 1+) FORMUL 5 HOH *421(H2 O) HELIX 1 1 ASP A 3 ASP A 13 1 11 HELIX 2 2 ASP A 15 ALA A 30 1 16 HELIX 3 3 ASP A 31 SER A 55 1 25 HELIX 4 4 PHE A 59 LYS A 78 1 20 HELIX 5 5 ASP A 103 SER A 116 1 14 HELIX 6 6 PRO A 128 ASN A 140 1 13 HELIX 7 7 LEU A 150 GLU A 167 1 18 HELIX 8 8 LEU A 169 LEU A 173 5 5 HELIX 9 9 ASN A 183 GLY A 191 1 9 HELIX 10 10 ASN A 198 VAL A 210 1 13 HELIX 11 11 ASP B 3 ASP B 13 1 11 HELIX 12 12 ASP B 15 ALA B 30 1 16 HELIX 13 13 ALA B 32 SER B 55 1 24 HELIX 14 14 PHE B 59 LYS B 78 1 20 HELIX 15 15 PRO B 79 LEU B 81 5 3 HELIX 16 16 ASP B 103 SER B 116 1 14 HELIX 17 17 PRO B 128 ASN B 140 1 13 HELIX 18 18 LEU B 150 GLU B 167 1 18 HELIX 19 19 LEU B 169 LEU B 173 5 5 HELIX 20 20 ASN B 183 GLY B 191 1 9 HELIX 21 21 ASN B 198 VAL B 210 1 13 SHEET 1 A 5 GLU A 119 ASP A 122 0 SHEET 2 A 5 LYS A 91 THR A 96 1 N ILE A 92 O PHE A 121 SHEET 3 A 5 ILE A 143 SER A 147 1 O GLY A 145 N VAL A 93 SHEET 4 A 5 LYS A 174 GLY A 178 1 O ILE A 176 N VAL A 144 SHEET 5 A 5 ASP A 194 PHE A 195 1 O ASP A 194 N ILE A 177 SHEET 1 B 5 GLU B 119 ASP B 122 0 SHEET 2 B 5 LYS B 91 THR B 96 1 N ILE B 92 O PHE B 121 SHEET 3 B 5 ILE B 143 SER B 147 1 O GLY B 145 N VAL B 93 SHEET 4 B 5 LYS B 174 GLY B 178 1 O ILE B 176 N VAL B 144 SHEET 5 B 5 ASP B 194 SER B 196 1 O SER B 196 N ILE B 177 LINK NE2 HIS A 102 CO COB A 301 1555 1555 2.56 LINK NE2 HIS B 102 CO COB B 301 1555 1555 2.48 SITE 1 AC1 38 LEU A 63 GLY A 99 ASP A 100 LEU A 101 SITE 2 AC1 38 HIS A 102 ASP A 103 ILE A 104 GLY A 105 SITE 3 AC1 38 LYS A 106 PHE A 109 GLY A 145 LEU A 146 SITE 4 AC1 38 SER A 147 LEU A 150 GLY A 178 GLY A 179 SITE 5 AC1 38 VAL A 180 SER A 196 ASN A 198 ALA A 199 SITE 6 AC1 38 HOH A 406 HOH A 409 HOH A 426 HOH A 432 SITE 7 AC1 38 HOH A 439 HOH A 440 HOH A 441 HOH A 455 SITE 8 AC1 38 HOH A 457 HOH A 480 HOH A 487 HOH A 566 SITE 9 AC1 38 HOH A 572 HOH A 590 HOH A 596 GLU B 16 SITE 10 AC1 38 ASN B 20 PHE B 65 SITE 1 AC2 43 GLU A 16 ASN A 20 PHE A 65 HOH A 505 SITE 2 AC2 43 ILE B 60 LEU B 63 GLY B 99 ASP B 100 SITE 3 AC2 43 LEU B 101 HIS B 102 ASP B 103 ILE B 104 SITE 4 AC2 43 GLY B 105 PHE B 109 GLY B 145 LEU B 146 SITE 5 AC2 43 SER B 147 LEU B 150 GLY B 178 GLY B 179 SITE 6 AC2 43 VAL B 180 SER B 196 THR B 197 ASN B 198 SITE 7 AC2 43 ALA B 199 HOH B 401 HOH B 403 HOH B 404 SITE 8 AC2 43 HOH B 408 HOH B 410 HOH B 412 HOH B 420 SITE 9 AC2 43 HOH B 434 HOH B 455 HOH B 478 HOH B 479 SITE 10 AC2 43 HOH B 488 HOH B 494 HOH B 503 HOH B 533 SITE 11 AC2 43 HOH B 538 HOH B 542 HOH B 578 CRYST1 69.990 69.990 91.680 90.00 90.00 120.00 P 31 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 0.014288 0.008249 0.000000 0.00000 SCALE2 0.000000 0.016498 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010908 0.00000