HEADER TRANSFERASE 26-APR-07 2YXD TITLE CRYSTAL STRUCTURE OF COBALAMIN BIOSYNTHESIS PRECORRIN 8W DECARBOXYLASE TITLE 2 (CBIT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE COBALT-PRECORRIN-6Y C(15)-METHYLTRANSFERASE COMPND 3 [DECARBOXYLATING]; COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: COBALAMIN BIOSYNTHESIS PRECORRIN 8W DECARBOXYLASES; COMPND 6 EC: 2.1.1.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 243232; SOURCE 4 STRAIN: DSM 2661; SOURCE 5 GENE: CBIT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS (DE3)-RIL-X; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-21A KEYWDS ALPHA AND BETA PROTEIN (A/B) CLASS, METHYLTRANSFERASE SUPERFAMILY, KEYWDS 2 STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL KEYWDS 3 AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 4 INITIATIVE, RSGI, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR B.PADMANABHAN,Y.BESSHO,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 13-JUL-11 2YXD 1 VERSN REVDAT 2 24-FEB-09 2YXD 1 VERSN REVDAT 1 30-OCT-07 2YXD 0 JRNL AUTH B.PADMANABHAN,Y.BESSHO,S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF COBALAMIN BIOSYNTHESIS PRECORRIN 8W JRNL TITL 2 DECARBOXYLASE (CBIT) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 14721 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 788 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 896 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE SET COUNT : 57 REMARK 3 BIN FREE R VALUE : 0.3280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2763 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.80000 REMARK 3 B22 (A**2) : 1.80000 REMARK 3 B33 (A**2) : -3.60000 REMARK 3 B12 (A**2) : 0.00000 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): 0.453 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.289 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.212 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.744 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2815 ; 0.031 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3793 ; 2.486 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 358 ; 7.252 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;42.420 ;26.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 536 ;18.858 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;15.103 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 450 ; 0.195 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2026 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1422 ; 0.270 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1970 ; 0.333 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 147 ; 0.193 ; 0.200 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): 73 ; 0.320 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.175 ; 0.200 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): 1842 ; 1.553 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2886 ; 2.455 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1085 ; 4.139 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 907 ; 6.376 ; 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2YXD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JUL-07. REMARK 100 THE RCSB ID CODE IS RCSB027253. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97891, 0.90000, 0.97928 REMARK 200 MONOCHROMATOR : SI DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16322 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 12.600 REMARK 200 R MERGE (I) : 0.08900 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) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.4 REMARK 200 DATA REDUNDANCY IN SHELL : 9.60 REMARK 200 R MERGE FOR SHELL (I) : 0.36000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% PEG 400, 0.1M MES, PH 6.0, OIL REMARK 280 BATCH, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -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 40.52100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 46.72100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 46.72100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.26050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 46.72100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 46.72100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 60.78150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 46.72100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.72100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 20.26050 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 46.72100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.72100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 60.78150 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 40.52100 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -108.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 BIOMT1 2 0.000000 -1.000000 0.000000 93.44200 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 93.44200 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 40.52100 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 MSE A 1 REMARK 465 LYS A 2 REMARK 465 TYR A 3 REMARK 465 MSE B 1 REMARK 465 LYS B 2 REMARK 465 TYR B 3 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 MSE A 4 CG SE CE REMARK 470 ARG A 12 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 13 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 14 CG CD OE1 OE2 REMARK 470 TYR A 65 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 66 CG CD1 CD2 REMARK 470 LYS A 110 CG CD CE NZ REMARK 470 MSE B 4 CG SE CE REMARK 470 ARG B 12 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 13 CG CD NE CZ NH1 NH2 REMARK 470 TYR B 65 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 110 CG CD CE NZ 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 21 CG GLU A 21 CD 0.103 REMARK 500 VAL A 60 CB VAL A 60 CG2 -0.140 REMARK 500 VAL A 128 CB VAL A 128 CG1 0.149 REMARK 500 GLU B 145 CB GLU B 145 CG 0.312 REMARK 500 GLU B 145 CD GLU B 145 OE2 0.168 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 64 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 THR A 109 N - CA - C ANGL. DEV. = 18.9 DEGREES REMARK 500 ASP B 7 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG B 24 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 ASP B 67 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP B 67 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 GLU B 145 CG - CD - OE1 ANGL. DEV. = -20.5 DEGREES REMARK 500 GLU B 145 CG - CD - OE2 ANGL. DEV. = 17.9 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 5 -44.71 162.80 REMARK 500 PRO A 6 155.44 -16.80 REMARK 500 THR A 109 139.52 41.40 REMARK 500 ASN A 111 61.32 61.85 REMARK 500 ASN A 174 123.27 23.20 REMARK 500 ASP B 7 -105.63 -50.02 REMARK 500 GLU B 8 22.81 -153.35 REMARK 500 GLU B 9 25.49 -78.88 REMARK 500 GLU B 21 -50.45 -21.34 REMARK 500 ASN B 84 53.95 -92.83 REMARK 500 PHE B 101 160.57 179.24 REMARK 500 THR B 109 141.21 -170.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ILE A 5 22.4 L L OUTSIDE RANGE REMARK 500 THR A 109 21.7 L L OUTSIDE RANGE REMARK 500 ASN A 174 18.9 L L OUTSIDE RANGE REMARK 500 ASN B 111 24.6 L L OUTSIDE RANGE 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 A1037 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A1060 DISTANCE = 5.69 ANGSTROMS REMARK 525 HOH B2003 DISTANCE = 7.61 ANGSTROMS REMARK 525 HOH B2042 DISTANCE = 5.17 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES B 2001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MJA001000391.1 RELATED DB: TARGETDB DBREF 2YXD A 1 183 UNP Q57836 CBIT_METJA 1 183 DBREF 2YXD B 1 183 UNP Q57836 CBIT_METJA 1 183 SEQRES 1 A 183 MSE LYS TYR MSE ILE PRO ASP GLU GLU PHE ILE ARG ARG SEQRES 2 A 183 GLU GLY VAL PRO ILE THR LYS GLU GLU ILE ARG ALA VAL SEQRES 3 A 183 SER ILE GLY LYS LEU ASN LEU ASN LYS ASP ASP VAL VAL SEQRES 4 A 183 VAL ASP VAL GLY CYS GLY SER GLY GLY MSE THR VAL GLU SEQRES 5 A 183 ILE ALA LYS ARG CYS LYS PHE VAL TYR ALA ILE ASP TYR SEQRES 6 A 183 LEU ASP GLY ALA ILE GLU VAL THR LYS GLN ASN LEU ALA SEQRES 7 A 183 LYS PHE ASN ILE LYS ASN CYS GLN ILE ILE LYS GLY ARG SEQRES 8 A 183 ALA GLU ASP VAL LEU ASP LYS LEU GLU PHE ASN LYS ALA SEQRES 9 A 183 PHE ILE GLY GLY THR LYS ASN ILE GLU LYS ILE ILE GLU SEQRES 10 A 183 ILE LEU ASP LYS LYS LYS ILE ASN HIS ILE VAL ALA ASN SEQRES 11 A 183 THR ILE VAL LEU GLU ASN ALA ALA LYS ILE ILE ASN GLU SEQRES 12 A 183 PHE GLU SER ARG GLY TYR ASN VAL ASP ALA VAL ASN VAL SEQRES 13 A 183 PHE ILE SER TYR ALA LYS LYS ILE PRO SER GLY HIS MSE SEQRES 14 A 183 PHE LEU ALA LYS ASN PRO ILE THR ILE ILE LYS ALA VAL SEQRES 15 A 183 ARG SEQRES 1 B 183 MSE LYS TYR MSE ILE PRO ASP GLU GLU PHE ILE ARG ARG SEQRES 2 B 183 GLU GLY VAL PRO ILE THR LYS GLU GLU ILE ARG ALA VAL SEQRES 3 B 183 SER ILE GLY LYS LEU ASN LEU ASN LYS ASP ASP VAL VAL SEQRES 4 B 183 VAL ASP VAL GLY CYS GLY SER GLY GLY MSE THR VAL GLU SEQRES 5 B 183 ILE ALA LYS ARG CYS LYS PHE VAL TYR ALA ILE ASP TYR SEQRES 6 B 183 LEU ASP GLY ALA ILE GLU VAL THR LYS GLN ASN LEU ALA SEQRES 7 B 183 LYS PHE ASN ILE LYS ASN CYS GLN ILE ILE LYS GLY ARG SEQRES 8 B 183 ALA GLU ASP VAL LEU ASP LYS LEU GLU PHE ASN LYS ALA SEQRES 9 B 183 PHE ILE GLY GLY THR LYS ASN ILE GLU LYS ILE ILE GLU SEQRES 10 B 183 ILE LEU ASP LYS LYS LYS ILE ASN HIS ILE VAL ALA ASN SEQRES 11 B 183 THR ILE VAL LEU GLU ASN ALA ALA LYS ILE ILE ASN GLU SEQRES 12 B 183 PHE GLU SER ARG GLY TYR ASN VAL ASP ALA VAL ASN VAL SEQRES 13 B 183 PHE ILE SER TYR ALA LYS LYS ILE PRO SER GLY HIS MSE SEQRES 14 B 183 PHE LEU ALA LYS ASN PRO ILE THR ILE ILE LYS ALA VAL SEQRES 15 B 183 ARG MODRES 2YXD MSE A 4 MET SELENOMETHIONINE MODRES 2YXD MSE A 49 MET SELENOMETHIONINE MODRES 2YXD MSE A 169 MET SELENOMETHIONINE MODRES 2YXD MSE B 4 MET SELENOMETHIONINE MODRES 2YXD MSE B 49 MET SELENOMETHIONINE MODRES 2YXD MSE B 169 MET SELENOMETHIONINE HET MSE A 4 5 HET MSE A 49 8 HET MSE A 169 8 HET MSE B 4 5 HET MSE B 49 8 HET MSE B 169 8 HET SO4 A1001 5 HET SO4 B1002 5 HET MES B2001 12 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 MES C6 H13 N O4 S FORMUL 6 HOH *108(H2 O) HELIX 1 1 LYS A 20 ASN A 32 1 13 HELIX 2 2 GLY A 47 LYS A 55 1 9 HELIX 3 3 LEU A 66 PHE A 80 1 15 HELIX 4 4 ARG A 91 LEU A 96 1 6 HELIX 5 5 ASP A 97 LEU A 99 5 3 HELIX 6 6 ASN A 111 LYS A 122 1 12 HELIX 7 7 VAL A 133 ARG A 147 1 15 HELIX 8 8 LYS B 20 ASN B 32 1 13 HELIX 9 9 GLY B 47 LYS B 55 1 9 HELIX 10 10 LEU B 66 PHE B 80 1 15 HELIX 11 11 ARG B 91 LEU B 96 1 6 HELIX 12 12 ASP B 97 LEU B 99 5 3 HELIX 13 13 ASN B 111 LYS B 122 1 12 HELIX 14 14 VAL B 133 ARG B 147 1 15 SHEET 1 A14 CYS A 85 LYS A 89 0 SHEET 2 A14 PHE A 59 ASP A 64 1 N ALA A 62 O ILE A 88 SHEET 3 A14 VAL A 38 VAL A 42 1 N ASP A 41 O TYR A 61 SHEET 4 A14 LYS A 103 ILE A 106 1 O PHE A 105 N VAL A 42 SHEET 5 A14 HIS A 126 THR A 131 1 O VAL A 128 N ALA A 104 SHEET 6 A14 ILE A 176 VAL A 182 -1 O ILE A 179 N ALA A 129 SHEET 7 A14 ASN A 150 ILE A 164 -1 N ASN A 150 O VAL A 182 SHEET 8 A14 ASN B 150 ILE B 164 -1 O SER B 159 N ASN A 155 SHEET 9 A14 ILE B 176 VAL B 182 -1 O LYS B 180 N ASP B 152 SHEET 10 A14 HIS B 126 THR B 131 -1 N ALA B 129 O ILE B 179 SHEET 11 A14 LYS B 103 ILE B 106 1 N ILE B 106 O VAL B 128 SHEET 12 A14 VAL B 38 VAL B 42 1 N VAL B 40 O PHE B 105 SHEET 13 A14 PHE B 59 ASP B 64 1 O TYR B 61 N ASP B 41 SHEET 14 A14 CYS B 85 LYS B 89 1 O ILE B 88 N ALA B 62 SHEET 1 B 4 GLY A 167 ALA A 172 0 SHEET 2 B 4 ASN A 150 ILE A 164 -1 N TYR A 160 O LEU A 171 SHEET 3 B 4 ASN B 150 ILE B 164 -1 O SER B 159 N ASN A 155 SHEET 4 B 4 GLY B 167 ALA B 172 -1 O MSE B 169 N LYS B 162 LINK C MSE A 4 N ILE A 5 1555 1555 1.34 LINK C GLY A 48 N MSE A 49 1555 1555 1.32 LINK C MSE A 49 N THR A 50 1555 1555 1.32 LINK C HIS A 168 N MSE A 169 1555 1555 1.31 LINK C MSE A 169 N PHE A 170 1555 1555 1.34 LINK C MSE B 4 N ILE B 5 1555 1555 1.33 LINK C GLY B 48 N MSE B 49 1555 1555 1.31 LINK C MSE B 49 N THR B 50 1555 1555 1.33 LINK C HIS B 168 N MSE B 169 1555 1555 1.31 LINK C MSE B 169 N PHE B 170 1555 1555 1.30 SITE 1 AC1 8 PRO A 17 ILE A 18 THR A 19 SER A 46 SITE 2 AC1 8 GLY A 47 GLY A 48 MSE A 49 HOH A1056 SITE 1 AC2 6 ILE B 18 THR B 19 SER B 46 GLY B 47 SITE 2 AC2 6 GLY B 48 MSE B 49 SITE 1 AC3 7 ASN A 155 PHE A 170 THR B 131 LEU B 134 SITE 2 AC3 7 ASN B 155 PRO B 175 THR B 177 CRYST1 93.442 93.442 81.042 90.00 90.00 90.00 P 41 21 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 0.010702 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010702 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012339 0.00000 HETATM 1 N MSE A 4 68.447 17.862 46.777 1.00 74.72 N HETATM 2 CA MSE A 4 67.215 18.137 45.913 1.00 75.04 C HETATM 3 C MSE A 4 67.567 18.974 44.626 1.00 74.67 C HETATM 4 O MSE A 4 68.586 18.694 44.012 1.00 75.20 O HETATM 5 CB MSE A 4 66.037 18.735 46.768 1.00 74.73 C