PDB Short entry for 2BNG HEADER HYDROLASE 24-MAR-05 2BNG TITLE STRUCTURE OF AN M.TUBERCULOSIS LEH-LIKE EPOXIDE HYDROLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MB2760; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: LEH-LIKE EPOXIDE HYDROLASE; COMPND 5 EC: 3.3.2.8; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: ENDOGENOUS LIGAND OF UNKNOWN ORIGIN BOUND COMPND 8 IN THE ACTIVE SITE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS M.TUBERCULOSIS, EPOXIDE HYDROLASE, LIMONENE, HYDROLASE, KEYWDS 2 STRUCTURAL PROTEOMICS IN EUROPE, SPINE, STRUCTURAL KEYWDS 3 GENOMICS EXPDTA X-RAY DIFFRACTION AUTHOR P.JOHANSSON,M.ARAND,T.UNGE,T.BERGFORS,T.A.JONES,S.L.MOWBRAY REVDAT 4 24-FEB-09 2BNG 1 VERSN REVDAT 3 20-DEC-06 2BNG 1 JRNL REVDAT 2 10-AUG-05 2BNG 1 MTRIX1 MTRIX2 MTRIX3 REVDAT 1 03-AUG-05 2BNG 0 JRNL AUTH P.JOHANSSON,T.UNGE,A.CRONIN,M.ARAND,T.BERGFORS, JRNL AUTH 2 T.A.JONES,S.L.MOWBRAY JRNL TITL STRUCTURE OF AN ATYPICAL EPOXIDE HYDROLASE FROM JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS GIVES INSIGHTS INTO ITS JRNL TITL 3 FUNCTION. JRNL REF J.MOL.BIOL. V. 351 1048 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 16051262 JRNL DOI 10.1016/J.JMB.2005.06.055 REMARK 2 RESOLUTION. 2.5 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15394 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) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 812 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1119 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE SET COUNT : 51 REMARK 3 BIN FREE R VALUE : 0.3600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3145 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.03000 REMARK 3 B22 (A**2) : 1.03000 REMARK 3 B33 (A**2) : -1.55000 REMARK 3 B12 (A**2) : 0.52000 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): 0.681 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.298 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.911 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3246 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4394 ; 1.962 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 402 ; 7.045 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 163 ;32.557 ;22.270 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 537 ;20.840 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;22.097 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 502 ; 0.134 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2480 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1370 ; 0.226 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2182 ; 0.320 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 160 ; 0.190 ; 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): 54 ; 0.283 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.230 ; 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): 1991 ; 0.512 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3192 ; 1.014 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1255 ; 1.761 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1202 ; 2.959 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B C REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 14 A 144 1 REMARK 3 1 B 14 B 144 1 REMARK 3 1 C 14 C 144 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 1033 ; 0.27 ; 0.05 REMARK 3 TIGHT POSITIONAL 1 B (A): 1033 ; 0.27 ; 0.05 REMARK 3 TIGHT POSITIONAL 1 C (A): 1033 ; 0.25 ; 0.05 REMARK 3 TIGHT THERMAL 1 A (A**2): 1033 ; 0.48 ; 0.50 REMARK 3 TIGHT THERMAL 1 B (A**2): 1033 ; 0.49 ; 0.50 REMARK 3 TIGHT THERMAL 1 C (A**2): 1033 ; 0.49 ; 0.50 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 REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2BNG COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-MAR-05. REMARK 100 THE PDBE ID CODE IS EBI-23429. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 287.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : DIAMOND (111), GE(220) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16247 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 70.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 21.200 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 21.50 REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.3 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 78.01667 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 39.00833 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 39.00833 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 78.01667 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 GENERATING THE BIOMOLECULE 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 BIOMT1 2 -0.500000 -0.866025 0.000000 122.85150 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 70.92835 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 78.01706 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 ALA A 2 REMARK 465 GLU A 3 REMARK 465 LEU A 4 REMARK 465 THR A 5 REMARK 465 GLU A 6 REMARK 465 THR A 7 REMARK 465 SER A 8 REMARK 465 PRO A 9 REMARK 465 GLU A 10 REMARK 465 THR A 11 REMARK 465 PRO A 12 REMARK 465 LEU A 145 REMARK 465 LYS A 146 REMARK 465 ALA A 147 REMARK 465 THR A 148 REMARK 465 LEU A 149 REMARK 465 MSE B 1 REMARK 465 ALA B 2 REMARK 465 GLU B 3 REMARK 465 LEU B 4 REMARK 465 THR B 5 REMARK 465 GLU B 6 REMARK 465 THR B 7 REMARK 465 SER B 8 REMARK 465 PRO B 9 REMARK 465 GLU B 10 REMARK 465 THR B 11 REMARK 465 LEU B 145 REMARK 465 LYS B 146 REMARK 465 ALA B 147 REMARK 465 THR B 148 REMARK 465 LEU B 149 REMARK 465 MSE C 1 REMARK 465 ALA C 2 REMARK 465 GLU C 3 REMARK 465 LEU C 4 REMARK 465 THR C 5 REMARK 465 GLU C 6 REMARK 465 THR C 7 REMARK 465 SER C 8 REMARK 465 PRO C 9 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 NH2 ARG A 70 - CD ARG C 19 2.00 REMARK 500 O SER A 144 - O HOH A 2028 2.00 REMARK 500 NH1 ARG B 79 - OE2 GLU C 111 2.08 REMARK 500 REMARK 500 REMARK: NULL 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 VAL A 141 CB VAL A 141 CG1 -0.138 REMARK 500 VAL B 49 CB VAL B 49 CG1 -0.131 REMARK 500 ARG B 58 NE ARG B 58 CZ -0.086 REMARK 500 VAL B 141 CB VAL B 141 CG1 -0.230 REMARK 500 VAL B 141 CB VAL B 141 CG2 -0.187 REMARK 500 SER B 144 CA SER B 144 CB -0.097 REMARK 500 SER B 144 CA SER B 144 C -0.202 REMARK 500 VAL C 49 CB VAL C 49 CG1 -0.141 REMARK 500 VAL C 49 CB VAL C 49 CG2 -0.174 REMARK 500 ARG C 79 CZ ARG C 79 NH1 -0.083 REMARK 500 THR C 89 CB THR C 89 CG2 -0.199 REMARK 500 VAL C 141 CB VAL C 141 CG1 -0.134 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 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 19 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 GLU A 31 OE1 - CD - OE2 ANGL. DEV. = -9.9 DEGREES REMARK 500 ARG A 58 CA - CB - CG ANGL. DEV. = 15.9 DEGREES REMARK 500 ARG A 58 CG - CD - NE ANGL. DEV. = -23.0 DEGREES REMARK 500 ARG A 58 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 59 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 79 NE - CZ - NH2 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 116 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B 53 NE - CZ - NH1 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG B 55 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 58 CA - CB - CG ANGL. DEV. = -17.5 DEGREES REMARK 500 ARG B 58 CD - NE - CZ ANGL. DEV. = -12.1 DEGREES REMARK 500 ARG B 58 NE - CZ - NH1 ANGL. DEV. = -6.6 DEGREES REMARK 500 ARG B 58 NH1 - CZ - NH2 ANGL. DEV. = 8.2 DEGREES REMARK 500 ARG B 66 NE - CZ - NH1 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG B 66 NE - CZ - NH2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP B 83 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG B 135 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 VAL B 141 CG1 - CB - CG2 ANGL. DEV. = -15.5 DEGREES REMARK 500 SER B 144 CB - CA - C ANGL. DEV. = -14.3 DEGREES REMARK 500 SER B 144 N - CA - CB ANGL. DEV. = 14.2 DEGREES REMARK 500 ARG C 19 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG C 19 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 VAL C 49 CG1 - CB - CG2 ANGL. DEV. = -13.7 DEGREES REMARK 500 ARG C 55 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG C 58 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG C 66 NE - CZ - NH1 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG C 79 NE - CZ - NH2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP C 114 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG C 116 NE - CZ - NH2 ANGL. DEV. = 3.9 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 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 PRO A 143 84.94 -64.12 REMARK 500 PRO B 143 0.39 -54.58 REMARK 500 PRO C 143 -4.57 -56.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO B 143 SER B 144 146.91 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 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 VAL A 49 21.2 L L OUTSIDE RANGE REMARK 500 VAL B 49 20.9 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 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 CA B1145 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 13 OE1 REMARK 620 2 ASP B 114 OD2 166.4 REMARK 620 3 ASP A 42 OD1 108.5 79.4 REMARK 620 4 ASP A 42 OD2 67.2 121.6 42.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1146 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN B 29 O REMARK 620 2 GLU C 31 OE1 172.8 REMARK 620 3 GLU C 31 OE2 143.4 39.1 REMARK 620 4 GLN C 68 OE1 110.0 75.2 89.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B1145 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B1146 DBREF 2BNG A 1 149 UNP Q7TY00 Q7TY00_MYCBO 1 149 DBREF 2BNG B 1 149 UNP Q7TY00 Q7TY00_MYCBO 1 149 DBREF 2BNG C 1 149 UNP Q7TY00 Q7TY00_MYCBO 1 149 SEQRES 1 A 149 MSE ALA GLU LEU THR GLU THR SER PRO GLU THR PRO GLU SEQRES 2 A 149 THR THR GLU ALA ILE ARG ALA VAL GLU ALA PHE LEU ASN SEQRES 3 A 149 ALA LEU GLN ASN GLU ASP PHE ASP THR VAL ASP ALA ALA SEQRES 4 A 149 LEU GLY ASP ASP LEU VAL TYR GLU ASN VAL GLY PHE SER SEQRES 5 A 149 ARG ILE ARG GLY GLY ARG ARG THR ALA THR LEU LEU ARG SEQRES 6 A 149 ARG MSE GLN GLY ARG VAL GLY PHE GLU VAL LYS ILE HIS SEQRES 7 A 149 ARG ILE GLY ALA ASP GLY ALA ALA VAL LEU THR GLU ARG SEQRES 8 A 149 THR ASP ALA LEU ILE ILE GLY PRO LEU ARG VAL GLN PHE SEQRES 9 A 149 TRP VAL CYS GLY VAL PHE GLU VAL ASP ASP GLY ARG ILE SEQRES 10 A 149 THR LEU TRP ARG ASP TYR PHE ASP VAL TYR ASP MSE PHE SEQRES 11 A 149 LYS GLY LEU LEU ARG GLY LEU VAL ALA LEU VAL VAL PRO SEQRES 12 A 149 SER LEU LYS ALA THR LEU SEQRES 1 B 149 MSE ALA GLU LEU THR GLU THR SER PRO GLU THR PRO GLU SEQRES 2 B 149 THR THR GLU ALA ILE ARG ALA VAL GLU ALA PHE LEU ASN SEQRES 3 B 149 ALA LEU GLN ASN GLU ASP PHE ASP THR VAL ASP ALA ALA SEQRES 4 B 149 LEU GLY ASP ASP LEU VAL TYR GLU ASN VAL GLY PHE SER SEQRES 5 B 149 ARG ILE ARG GLY GLY ARG ARG THR ALA THR LEU LEU ARG SEQRES 6 B 149 ARG MSE GLN GLY ARG VAL GLY PHE GLU VAL LYS ILE HIS SEQRES 7 B 149 ARG ILE GLY ALA ASP GLY ALA ALA VAL LEU THR GLU ARG SEQRES 8 B 149 THR ASP ALA LEU ILE ILE GLY PRO LEU ARG VAL GLN PHE SEQRES 9 B 149 TRP VAL CYS GLY VAL PHE GLU VAL ASP ASP GLY ARG ILE SEQRES 10 B 149 THR LEU TRP ARG ASP TYR PHE ASP VAL TYR ASP MSE PHE SEQRES 11 B 149 LYS GLY LEU LEU ARG GLY LEU VAL ALA LEU VAL VAL PRO SEQRES 12 B 149 SER LEU LYS ALA THR LEU SEQRES 1 C 149 MSE ALA GLU LEU THR GLU THR SER PRO GLU THR PRO GLU SEQRES 2 C 149 THR THR GLU ALA ILE ARG ALA VAL GLU ALA PHE LEU ASN SEQRES 3 C 149 ALA LEU GLN ASN GLU ASP PHE ASP THR VAL ASP ALA ALA SEQRES 4 C 149 LEU GLY ASP ASP LEU VAL TYR GLU ASN VAL GLY PHE SER SEQRES 5 C 149 ARG ILE ARG GLY GLY ARG ARG THR ALA THR LEU LEU ARG SEQRES 6 C 149 ARG MSE GLN GLY ARG VAL GLY PHE GLU VAL LYS ILE HIS SEQRES 7 C 149 ARG ILE GLY ALA ASP GLY ALA ALA VAL LEU THR GLU ARG SEQRES 8 C 149 THR ASP ALA LEU ILE ILE GLY PRO LEU ARG VAL GLN PHE SEQRES 9 C 149 TRP VAL CYS GLY VAL PHE GLU VAL ASP ASP GLY ARG ILE SEQRES 10 C 149 THR LEU TRP ARG ASP TYR PHE ASP VAL TYR ASP MSE PHE SEQRES 11 C 149 LYS GLY LEU LEU ARG GLY LEU VAL ALA LEU VAL VAL PRO SEQRES 12 C 149 SER LEU LYS ALA THR LEU MODRES 2BNG MSE A 67 MET SELENOMETHIONINE MODRES 2BNG MSE A 129 MET SELENOMETHIONINE MODRES 2BNG MSE B 67 MET SELENOMETHIONINE MODRES 2BNG MSE B 129 MET SELENOMETHIONINE MODRES 2BNG MSE C 67 MET SELENOMETHIONINE MODRES 2BNG MSE C 129 MET SELENOMETHIONINE HET MSE A 67 8 HET MSE A 129 8 HET MSE B 67 8 HET MSE B 129 8 HET MSE C 67 8 HET MSE C 129 8 HET CA B1145 1 HET CA B1146 1 HETNAM MSE SELENOMETHIONINE HETNAM CA CALCIUM ION FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 4 CA 2(CA 2+) FORMUL 6 HOH *89(H2 O1) HELIX 1 1 GLU A 13 GLU A 31 1 19 HELIX 2 2 ASP A 32 ALA A 39 1 8 HELIX 3 3 GLY A 56 ARG A 66 1 11 HELIX 4 4 ASP A 125 LEU A 140 1 16 HELIX 5 5 PRO B 12 GLU B 31 1 20 HELIX 6 6 ASP B 32 ALA B 39 1 8 HELIX 7 7 GLY B 56 ARG B 66 1 11 HELIX 8 8 PHE B 130 LEU B 140 1 11 HELIX 9 9 PRO C 12 GLU C 31 1 20 HELIX 10 10 ASP C 32 ALA C 39 1 8 HELIX 11 11 GLY C 56 ARG C 66 1 11 HELIX 12 12 ASP C 125 LEU C 140 1 16 HELIX 13 13 VAL C 142 LYS C 146 5 5 SHEET 1 AA 6 SER A 52 ARG A 55 0 SHEET 2 AA 6 LEU A 40 ASN A 48 -1 O TYR A 46 N ILE A 54 SHEET 3 AA 6 ARG A 116 TYR A 123 1 O ILE A 117 N GLY A 41 SHEET 4 AA 6 LEU A 100 ASP A 113 -1 O CYS A 107 N TYR A 123 SHEET 5 AA 6 ALA A 86 ILE A 97 -1 O VAL A 87 N PHE A 110 SHEET 6 AA 6 GLY A 72 ASP A 83 -1 O GLY A 72 N ILE A 96 SHEET 1 BA 6 SER B 52 ARG B 55 0 SHEET 2 BA 6 LEU B 40 ASN B 48 -1 O TYR B 46 N ILE B 54 SHEET 3 BA 6 ARG B 116 TYR B 123 1 O ILE B 117 N GLY B 41 SHEET 4 BA 6 LEU B 100 ASP B 113 -1 O CYS B 107 N TYR B 123 SHEET 5 BA 6 ALA B 86 ILE B 97 -1 O VAL B 87 N PHE B 110 SHEET 6 BA 6 GLY B 72 ASP B 83 -1 O GLY B 72 N ILE B 96 SHEET 1 CA 6 SER C 52 ARG C 55 0 SHEET 2 CA 6 LEU C 40 ASN C 48 -1 O TYR C 46 N ILE C 54 SHEET 3 CA 6 ARG C 116 TYR C 123 1 O ILE C 117 N GLY C 41 SHEET 4 CA 6 LEU C 100 ASP C 113 -1 O CYS C 107 N TYR C 123 SHEET 5 CA 6 ALA C 86 ILE C 97 -1 O VAL C 87 N PHE C 110 SHEET 6 CA 6 GLY C 72 ASP C 83 -1 O GLY C 72 N ILE C 96 LINK C ARG A 66 N MSE A 67 1555 1555 1.33 LINK C MSE A 67 N GLN A 68 1555 1555 1.33 LINK C ASP A 128 N MSE A 129 1555 1555 1.33 LINK C MSE A 129 N PHE A 130 1555 1555 1.33 LINK C ARG B 66 N MSE B 67 1555 1555 1.32 LINK C MSE B 67 N GLN B 68 1555 1555 1.32 LINK C ASP B 128 N MSE B 129 1555 1555 1.33 LINK C MSE B 129 N PHE B 130 1555 1555 1.33 LINK CA CA B1145 OD2 ASP A 42 1555 1555 3.22 LINK CA CA B1145 OD1 ASP A 42 1555 1555 2.59 LINK CA CA B1145 OD2 ASP B 114 1555 1555 2.59 LINK CA CA B1145 OE1 GLU B 13 1555 1555 2.84 LINK CA CA B1146 OE1 GLN C 68 1555 4456 2.59 LINK CA CA B1146 OE2 GLU C 31 1555 4456 3.24 LINK CA CA B1146 OE1 GLU C 31 1555 4456 2.05 LINK CA CA B1146 O GLN B 29 1555 1555 2.39 LINK C ARG C 66 N MSE C 67 1555 1555 1.32 LINK C MSE C 67 N GLN C 68 1555 1555 1.32 LINK C ASP C 128 N MSE C 129 1555 1555 1.33 LINK C MSE C 129 N PHE C 130 1555 1555 1.32 SITE 1 AC1 3 ASP A 42 GLU B 13 ASP B 114 SITE 1 AC2 3 GLN B 29 GLU C 31 GLN C 68 CRYST1 81.901 81.901 117.025 90.00 90.00 120.00 P 32 2 1 18 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 0.012210 0.007049 0.000000 0.00000 SCALE2 0.000000 0.014099 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008545 0.00000 MTRIX1 1 0.002300 -0.623200 0.782000 16.98730 1 MTRIX2 1 0.567400 0.644800 0.512200 -26.18150 1 MTRIX3 1 -0.823500 0.442600 0.355100 43.42450 1 MTRIX1 2 0.525400 -0.269700 -0.807000 31.85050 1 MTRIX2 2 -0.850600 -0.144300 -0.505600 127.31550 1 MTRIX3 2 0.019900 0.952100 -0.305200 -1.80380 1