HEADER ISOMERASE 10-JUN-08 2VVQ TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS RIBOSE-5-PHOSPHATE TITLE 2 ISOMERASE B IN COMPLEX WITH THE INHIBITOR 5-DEOXY-5-PHOSPHO-D- TITLE 3 RIBONATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSE-5-PHOSPHATE ISOMERASE B; COMPND 3 CHAIN: A, B, C, D, E; COMPND 4 SYNONYM: RIBOSE-5-PHOSPHATE ISOMERASE, PHOSPHORIBOISOMERASE B; COMPND 5 EC: 5.3.1.6; COMPND 6 ENGINEERED: YES 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: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PCRT7 KEYWDS PENTOSE PHOSPHATE PATHWAY, RPIB, RV2465C, ISOMERASE, CARBOHYDRATE KEYWDS 2 METABOLISM EXPDTA X-RAY DIFFRACTION AUTHOR E.KOWALINSKI,A.K.ROOS,S.MARIANO,L.SALMON,S.L.MOWBRAY REVDAT 5 13-DEC-23 2VVQ 1 REMARK REVDAT 4 24-FEB-09 2VVQ 1 VERSN REVDAT 3 09-SEP-08 2VVQ 1 JRNL REVDAT 2 29-JUL-08 2VVQ 1 AUTHOR REMARK REVDAT 1 01-JUL-08 2VVQ 0 JRNL AUTH A.K.ROOS,S.MARIANO,E.KOWALINSKI,L.SALMON,S.L.MOWBRAY JRNL TITL D-RIBOSE-5-PHOSPHATE ISOMERASE B FROM ESCHERICHIA COLI IS JRNL TITL 2 ALSO A FUNCTIONAL D-ALLOSE-6-PHOSPHATE ISOMERASE, WHILE THE JRNL TITL 3 MYCOBACTERIUM TUBERCULOSIS ENZYME IS NOT. JRNL REF J.MOL.BIOL. V. 382 667 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18640127 JRNL DOI 10.1016/J.JMB.2008.06.090 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 59767 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3193 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4383 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1950 REMARK 3 BIN FREE R VALUE SET COUNT : 206 REMARK 3 BIN FREE R VALUE : 0.2640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5915 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 85 REMARK 3 SOLVENT ATOMS : 547 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.48000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.41000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.37000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.144 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.131 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.086 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.015 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6113 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 4048 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8317 ; 1.408 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9816 ; 1.008 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 778 ; 6.334 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 280 ;29.579 ;23.214 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 921 ;12.943 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 55 ;19.353 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 917 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6941 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1228 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1286 ; 0.237 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4267 ; 0.202 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2926 ; 0.169 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 3042 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 475 ; 0.138 ; 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): 14 ; 0.131 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 59 ; 0.327 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 32 ; 0.150 ; 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): 4001 ; 1.458 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6165 ; 2.077 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2396 ; 1.454 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2152 ; 2.270 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 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. REMARK 4 REMARK 4 2VVQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1290036517. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-05 REMARK 200 TEMPERATURE (KELVIN) : 110 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 : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.94 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62962 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 81.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC 5 REMARK 200 STARTING MODEL: PDB ENTRY 1USL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 8000,0.1 M MES PH6, 5% PEG REMARK 280 1000, 0.2 M LISO4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 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 1.000000 0.000000 0.000000 68.18450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.05950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 68.18450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 51.05950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 5150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.1 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 5290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 5190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E 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 128.87597 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 69.19950 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2042 LIES ON A SPECIAL POSITION. 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 MET A 1 REMARK 465 SER A 2 REMARK 465 ALA A 160 REMARK 465 PRO A 161 REMARK 465 ALA A 162 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 ALA B 160 REMARK 465 PRO B 161 REMARK 465 ALA B 162 REMARK 465 MET C 1 REMARK 465 SER C 2 REMARK 465 ALA C 162 REMARK 465 MET D 1 REMARK 465 ALA D 160 REMARK 465 PRO D 161 REMARK 465 ALA D 162 REMARK 465 MET E 1 REMARK 465 SER E 2 REMARK 465 ALA E 160 REMARK 465 PRO E 161 REMARK 465 ALA E 162 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 GLY A 159 CA C O REMARK 470 GLY B 159 CA C O REMARK 470 PRO C 161 CA C O CB CG CD REMARK 470 GLY D 159 CA C O REMARK 470 GLY E 159 CA C O 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 B 68 CA - CB - CG ANGL. DEV. = 15.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE R10 A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE R10 B 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE R10 C 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE R10 D 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE R10 E 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BES RELATED DB: PDB REMARK 900 STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS RIBOSE- 5-PHOSPHATE REMARK 900 ISOMERASE, RPIB, RV2465C, IN COMPLEX WITH 4-PHOSPHO-D- REMARK 900 ERYTHRONOHYDROXAMIC ACID. REMARK 900 RELATED ID: 1USL RELATED DB: PDB REMARK 900 STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS RIBOSE- 5-PHOSPHATE REMARK 900 ISOMERASE, RPIB, RV2465C, COMPLEXED WITH PHOSPHATE. REMARK 900 RELATED ID: 2BET RELATED DB: PDB REMARK 900 STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS RIBOSE- 5-PHOSPHATE REMARK 900 ISOMERASE, RPIB, RV2465C, IN COMPLEX WITH 4-PHOSPHO-D-ERYTHRONATE. REMARK 900 RELATED ID: 2VVO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS RIBOSE-5-PHOSPHATE REMARK 900 ISOMERASE B IN COMPLEX WITH ALPHA ALLOSE 6-PHOSPHATE REMARK 900 RELATED ID: 2VVP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS RIBOSE-5-PHOSPHATE REMARK 900 ISOMERASE B IN COMPLEX WITH ITS SUBSTRATES RIBOSE 5-PHOSPHATE AND REMARK 900 RIBULOSE 5-PHOSPHATE REMARK 900 RELATED ID: 2VVR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE H99N MUTANT OF RIBOSE-5-PHOSPHATE REMARK 900 ISOMERASE B FROM E. COLI DBREF 2VVQ A 1 162 UNP Q79FD7 RPIB_MYCTU 1 162 DBREF 2VVQ B 1 162 UNP Q79FD7 RPIB_MYCTU 1 162 DBREF 2VVQ C 1 162 UNP Q79FD7 RPIB_MYCTU 1 162 DBREF 2VVQ D 1 162 UNP Q79FD7 RPIB_MYCTU 1 162 DBREF 2VVQ E 1 162 UNP Q79FD7 RPIB_MYCTU 1 162 SEQRES 1 A 162 MET SER GLY MET ARG VAL TYR LEU GLY ALA ASP HIS ALA SEQRES 2 A 162 GLY TYR GLU LEU LYS GLN ARG ILE ILE GLU HIS LEU LYS SEQRES 3 A 162 GLN THR GLY HIS GLU PRO ILE ASP CYS GLY ALA LEU ARG SEQRES 4 A 162 TYR ASP ALA ASP ASP ASP TYR PRO ALA PHE CYS ILE ALA SEQRES 5 A 162 ALA ALA THR ARG THR VAL ALA ASP PRO GLY SER LEU GLY SEQRES 6 A 162 ILE VAL LEU GLY GLY SER GLY ASN GLY GLU GLN ILE ALA SEQRES 7 A 162 ALA ASN LYS VAL PRO GLY ALA ARG CYS ALA LEU ALA TRP SEQRES 8 A 162 SER VAL GLN THR ALA ALA LEU ALA ARG GLU HIS ASN ASN SEQRES 9 A 162 ALA GLN LEU ILE GLY ILE GLY GLY ARG MET HIS THR VAL SEQRES 10 A 162 ALA GLU ALA LEU ALA ILE VAL ASP ALA PHE VAL THR THR SEQRES 11 A 162 PRO TRP SER LYS ALA GLN ARG HIS GLN ARG ARG ILE ASP SEQRES 12 A 162 ILE LEU ALA GLU TYR GLU ARG THR HIS GLU ALA PRO PRO SEQRES 13 A 162 VAL PRO GLY ALA PRO ALA SEQRES 1 B 162 MET SER GLY MET ARG VAL TYR LEU GLY ALA ASP HIS ALA SEQRES 2 B 162 GLY TYR GLU LEU LYS GLN ARG ILE ILE GLU HIS LEU LYS SEQRES 3 B 162 GLN THR GLY HIS GLU PRO ILE ASP CYS GLY ALA LEU ARG SEQRES 4 B 162 TYR ASP ALA ASP ASP ASP TYR PRO ALA PHE CYS ILE ALA SEQRES 5 B 162 ALA ALA THR ARG THR VAL ALA ASP PRO GLY SER LEU GLY SEQRES 6 B 162 ILE VAL LEU GLY GLY SER GLY ASN GLY GLU GLN ILE ALA SEQRES 7 B 162 ALA ASN LYS VAL PRO GLY ALA ARG CYS ALA LEU ALA TRP SEQRES 8 B 162 SER VAL GLN THR ALA ALA LEU ALA ARG GLU HIS ASN ASN SEQRES 9 B 162 ALA GLN LEU ILE GLY ILE GLY GLY ARG MET HIS THR VAL SEQRES 10 B 162 ALA GLU ALA LEU ALA ILE VAL ASP ALA PHE VAL THR THR SEQRES 11 B 162 PRO TRP SER LYS ALA GLN ARG HIS GLN ARG ARG ILE ASP SEQRES 12 B 162 ILE LEU ALA GLU TYR GLU ARG THR HIS GLU ALA PRO PRO SEQRES 13 B 162 VAL PRO GLY ALA PRO ALA SEQRES 1 C 162 MET SER GLY MET ARG VAL TYR LEU GLY ALA ASP HIS ALA SEQRES 2 C 162 GLY TYR GLU LEU LYS GLN ARG ILE ILE GLU HIS LEU LYS SEQRES 3 C 162 GLN THR GLY HIS GLU PRO ILE ASP CYS GLY ALA LEU ARG SEQRES 4 C 162 TYR ASP ALA ASP ASP ASP TYR PRO ALA PHE CYS ILE ALA SEQRES 5 C 162 ALA ALA THR ARG THR VAL ALA ASP PRO GLY SER LEU GLY SEQRES 6 C 162 ILE VAL LEU GLY GLY SER GLY ASN GLY GLU GLN ILE ALA SEQRES 7 C 162 ALA ASN LYS VAL PRO GLY ALA ARG CYS ALA LEU ALA TRP SEQRES 8 C 162 SER VAL GLN THR ALA ALA LEU ALA ARG GLU HIS ASN ASN SEQRES 9 C 162 ALA GLN LEU ILE GLY ILE GLY GLY ARG MET HIS THR VAL SEQRES 10 C 162 ALA GLU ALA LEU ALA ILE VAL ASP ALA PHE VAL THR THR SEQRES 11 C 162 PRO TRP SER LYS ALA GLN ARG HIS GLN ARG ARG ILE ASP SEQRES 12 C 162 ILE LEU ALA GLU TYR GLU ARG THR HIS GLU ALA PRO PRO SEQRES 13 C 162 VAL PRO GLY ALA PRO ALA SEQRES 1 D 162 MET SER GLY MET ARG VAL TYR LEU GLY ALA ASP HIS ALA SEQRES 2 D 162 GLY TYR GLU LEU LYS GLN ARG ILE ILE GLU HIS LEU LYS SEQRES 3 D 162 GLN THR GLY HIS GLU PRO ILE ASP CYS GLY ALA LEU ARG SEQRES 4 D 162 TYR ASP ALA ASP ASP ASP TYR PRO ALA PHE CYS ILE ALA SEQRES 5 D 162 ALA ALA THR ARG THR VAL ALA ASP PRO GLY SER LEU GLY SEQRES 6 D 162 ILE VAL LEU GLY GLY SER GLY ASN GLY GLU GLN ILE ALA SEQRES 7 D 162 ALA ASN LYS VAL PRO GLY ALA ARG CYS ALA LEU ALA TRP SEQRES 8 D 162 SER VAL GLN THR ALA ALA LEU ALA ARG GLU HIS ASN ASN SEQRES 9 D 162 ALA GLN LEU ILE GLY ILE GLY GLY ARG MET HIS THR VAL SEQRES 10 D 162 ALA GLU ALA LEU ALA ILE VAL ASP ALA PHE VAL THR THR SEQRES 11 D 162 PRO TRP SER LYS ALA GLN ARG HIS GLN ARG ARG ILE ASP SEQRES 12 D 162 ILE LEU ALA GLU TYR GLU ARG THR HIS GLU ALA PRO PRO SEQRES 13 D 162 VAL PRO GLY ALA PRO ALA SEQRES 1 E 162 MET SER GLY MET ARG VAL TYR LEU GLY ALA ASP HIS ALA SEQRES 2 E 162 GLY TYR GLU LEU LYS GLN ARG ILE ILE GLU HIS LEU LYS SEQRES 3 E 162 GLN THR GLY HIS GLU PRO ILE ASP CYS GLY ALA LEU ARG SEQRES 4 E 162 TYR ASP ALA ASP ASP ASP TYR PRO ALA PHE CYS ILE ALA SEQRES 5 E 162 ALA ALA THR ARG THR VAL ALA ASP PRO GLY SER LEU GLY SEQRES 6 E 162 ILE VAL LEU GLY GLY SER GLY ASN GLY GLU GLN ILE ALA SEQRES 7 E 162 ALA ASN LYS VAL PRO GLY ALA ARG CYS ALA LEU ALA TRP SEQRES 8 E 162 SER VAL GLN THR ALA ALA LEU ALA ARG GLU HIS ASN ASN SEQRES 9 E 162 ALA GLN LEU ILE GLY ILE GLY GLY ARG MET HIS THR VAL SEQRES 10 E 162 ALA GLU ALA LEU ALA ILE VAL ASP ALA PHE VAL THR THR SEQRES 11 E 162 PRO TRP SER LYS ALA GLN ARG HIS GLN ARG ARG ILE ASP SEQRES 12 E 162 ILE LEU ALA GLU TYR GLU ARG THR HIS GLU ALA PRO PRO SEQRES 13 E 162 VAL PRO GLY ALA PRO ALA HET R10 A 200 15 HET SO4 A 300 5 HET R10 B 200 15 HET R10 C 200 15 HET SO4 C 300 5 HET R10 D 200 15 HET R10 E 200 15 HETNAM R10 5-O-PHOSPHONO-D-RIBONIC ACID HETNAM SO4 SULFATE ION FORMUL 6 R10 5(C5 H11 O9 P) FORMUL 7 SO4 2(O4 S 2-) FORMUL 13 HOH *547(H2 O) HELIX 1 1 GLY A 14 THR A 28 1 15 HELIX 2 2 TYR A 46 ASP A 60 1 15 HELIX 3 3 GLY A 72 LYS A 81 1 10 HELIX 4 4 SER A 92 HIS A 102 1 11 HELIX 5 5 THR A 116 THR A 130 1 15 HELIX 6 6 ALA A 135 HIS A 152 1 18 HELIX 7 7 ASP B 11 THR B 28 1 18 HELIX 8 8 TYR B 46 ASP B 60 1 15 HELIX 9 9 GLY B 72 LYS B 81 1 10 HELIX 10 10 SER B 92 HIS B 102 1 11 HELIX 11 11 THR B 116 THR B 130 1 15 HELIX 12 12 ALA B 135 HIS B 152 1 18 HELIX 13 13 GLY C 14 THR C 28 1 15 HELIX 14 14 TYR C 46 ASP C 60 1 15 HELIX 15 15 GLY C 72 LYS C 81 1 10 HELIX 16 16 SER C 92 ASN C 104 1 13 HELIX 17 17 THR C 116 THR C 130 1 15 HELIX 18 18 ALA C 135 HIS C 152 1 18 HELIX 19 19 GLY D 14 THR D 28 1 15 HELIX 20 20 TYR D 46 ASP D 60 1 15 HELIX 21 21 GLY D 72 LYS D 81 1 10 HELIX 22 22 SER D 92 HIS D 102 1 11 HELIX 23 23 THR D 116 THR D 130 1 15 HELIX 24 24 ALA D 135 HIS D 152 1 18 HELIX 25 25 GLY E 14 THR E 28 1 15 HELIX 26 26 TYR E 46 ALA E 59 1 14 HELIX 27 27 GLY E 72 LYS E 81 1 10 HELIX 28 28 SER E 92 HIS E 102 1 11 HELIX 29 29 THR E 116 THR E 130 1 15 HELIX 30 30 ALA E 135 HIS E 152 1 18 SHEET 1 AA 5 GLU A 31 ASP A 34 0 SHEET 2 AA 5 ARG A 5 ALA A 10 1 O VAL A 6 N ILE A 33 SHEET 3 AA 5 LEU A 64 GLY A 69 1 O LEU A 64 N TYR A 7 SHEET 4 AA 5 LEU A 107 GLY A 111 1 O ILE A 108 N VAL A 67 SHEET 5 AA 5 CYS A 87 LEU A 89 1 O ALA A 88 N GLY A 109 SHEET 1 BA 5 GLU B 31 ASP B 34 0 SHEET 2 BA 5 ARG B 5 ALA B 10 1 O VAL B 6 N ILE B 33 SHEET 3 BA 5 LEU B 64 GLY B 69 1 O LEU B 64 N TYR B 7 SHEET 4 BA 5 LEU B 107 GLY B 111 1 O ILE B 108 N VAL B 67 SHEET 5 BA 5 CYS B 87 LEU B 89 1 O ALA B 88 N GLY B 109 SHEET 1 CA 5 GLU C 31 ASP C 34 0 SHEET 2 CA 5 ARG C 5 ALA C 10 1 O VAL C 6 N ILE C 33 SHEET 3 CA 5 LEU C 64 GLY C 69 1 O LEU C 64 N TYR C 7 SHEET 4 CA 5 LEU C 107 GLY C 111 1 O ILE C 108 N VAL C 67 SHEET 5 CA 5 CYS C 87 LEU C 89 1 O ALA C 88 N GLY C 109 SHEET 1 DA 5 GLU D 31 ASP D 34 0 SHEET 2 DA 5 ARG D 5 ALA D 10 1 O VAL D 6 N ILE D 33 SHEET 3 DA 5 LEU D 64 GLY D 69 1 O LEU D 64 N TYR D 7 SHEET 4 DA 5 LEU D 107 GLY D 111 1 O ILE D 108 N VAL D 67 SHEET 5 DA 5 CYS D 87 LEU D 89 1 O ALA D 88 N GLY D 109 SHEET 1 EA 5 GLU E 31 ASP E 34 0 SHEET 2 EA 5 ARG E 5 ALA E 10 1 O VAL E 6 N ILE E 33 SHEET 3 EA 5 LEU E 64 GLY E 69 1 O LEU E 64 N TYR E 7 SHEET 4 EA 5 LEU E 107 GLY E 111 1 O ILE E 108 N VAL E 67 SHEET 5 EA 5 CYS E 87 LEU E 89 1 O ALA E 88 N GLY E 109 CISPEP 1 GLY A 3 MET A 4 0 16.66 CISPEP 2 GLY A 36 ALA A 37 0 -0.47 CISPEP 3 GLY B 36 ALA B 37 0 3.55 CISPEP 4 GLY C 36 ALA C 37 0 1.68 CISPEP 5 GLY D 36 ALA D 37 0 6.54 CISPEP 6 GLY E 36 ALA E 37 0 1.10 SITE 1 AC1 20 ASP A 11 HIS A 12 TYR A 46 GLY A 69 SITE 2 AC1 20 GLY A 70 SER A 71 GLY A 72 ASN A 73 SITE 3 AC1 20 GLY A 74 GLU A 75 ARG A 113 HOH A2033 SITE 4 AC1 20 HOH A2107 HOH A2108 HOH A2109 HIS B 102 SITE 5 AC1 20 ASN B 103 ARG B 137 ARG B 141 HOH C2084 SITE 1 AC2 6 HOH A2110 HOH A2111 HOH A2112 HIS B 152 SITE 2 AC2 6 ARG D 5 HOH D2046 SITE 1 AC3 20 HIS A 102 ASN A 103 ARG A 137 ARG A 141 SITE 2 AC3 20 HOH A2084 ASP B 11 HIS B 12 TYR B 46 SITE 3 AC3 20 GLY B 69 GLY B 70 SER B 71 GLY B 72 SITE 4 AC3 20 ASN B 73 GLY B 74 GLU B 75 ARG B 113 SITE 5 AC3 20 HOH B2028 HOH B2113 HOH B2114 HOH B2115 SITE 1 AC4 19 ASP C 11 HIS C 12 TYR C 46 GLY C 69 SITE 2 AC4 19 GLY C 70 SER C 71 GLY C 72 ASN C 73 SITE 3 AC4 19 GLY C 74 GLU C 75 ARG C 113 HOH C2028 SITE 4 AC4 19 HOH C2113 HOH C2114 HOH C2115 HIS D 102 SITE 5 AC4 19 ARG D 137 ARG D 141 HOH D2098 SITE 1 AC5 4 ARG B 5 HOH C2116 HIS D 152 HOH D2116 SITE 1 AC6 19 HIS C 102 ASN C 103 ARG C 137 ARG C 141 SITE 2 AC6 19 HOH C2087 ASP D 11 HIS D 12 TYR D 46 SITE 3 AC6 19 GLY D 69 GLY D 70 SER D 71 GLY D 72 SITE 4 AC6 19 ASN D 73 GLY D 74 GLU D 75 ARG D 113 SITE 5 AC6 19 HOH D2027 HOH D2121 HOH D2122 SITE 1 AC7 19 ASP E 11 HIS E 12 TYR E 46 GLY E 69 SITE 2 AC7 19 GLY E 70 SER E 71 GLY E 72 ASN E 73 SITE 3 AC7 19 GLY E 74 GLU E 75 HIS E 102 ASN E 103 SITE 4 AC7 19 ARG E 113 ARG E 137 ARG E 141 HOH E2019 SITE 5 AC7 19 HOH E2070 HOH E2084 HOH E2085 CRYST1 136.369 102.119 69.604 90.00 96.18 90.00 C 1 2 1 20 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 0.007333 0.000000 0.000794 0.00000 SCALE2 0.000000 0.009792 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014451 0.00000 MTRIX1 1 -0.393590 0.913230 0.105330 22.03996 1 MTRIX2 1 0.912200 0.373790 0.167870 -16.93469 1 MTRIX3 1 0.113930 0.162160 -0.980170 19.20143 1 MTRIX1 2 -0.354130 -0.925530 0.134070 38.73606 1 MTRIX2 2 -0.923310 0.323240 -0.207410 34.63326 1 MTRIX3 2 0.148630 -0.197240 -0.969020 50.30714 1 MTRIX1 3 -0.689490 -0.648040 -0.323490 49.16639 1 MTRIX2 3 0.637320 -0.755020 0.154130 4.88663 1 MTRIX3 3 -0.344130 -0.099900 0.933590 38.24229 1 MTRIX1 4 -0.758530 0.547090 -0.354010 80.79425 1 MTRIX2 4 -0.550880 -0.828560 -0.100090 5.48696 1 MTRIX3 4 -0.348080 0.119090 0.929870 30.44961 1