HEADER ISOMERASE 10-JUN-08 2VVP TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS RIBOSE-5-PHOSPHATE TITLE 2 ISOMERASE B IN COMPLEX WITH ITS SUBSTRATES RIBOSE 5-PHOSPHATE AND TITLE 3 RIBULOSE 5-PHOSPHATE 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 RPIB, RV2465C, ISOMERASE, RARE SUGAR, CARBOHYDRATE METABOLISM, KEYWDS 2 PENTOSE PHOSPHATE PATHWAY EXPDTA X-RAY DIFFRACTION AUTHOR E.KOWALINSKI,A.K.ROOS,S.MARIANO,L.SALMON,S.L.MOWBRAY REVDAT 5 13-DEC-23 2VVP 1 REMARK REVDAT 4 24-FEB-09 2VVP 1 VERSN REVDAT 3 09-SEP-08 2VVP 1 JRNL REVDAT 2 29-JUL-08 2VVP 1 AUTHOR REVDAT 1 01-JUL-08 2VVP 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. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 109551 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5805 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8015 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE SET COUNT : 441 REMARK 3 BIN FREE R VALUE : 0.2940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5929 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 140 REMARK 3 SOLVENT ATOMS : 981 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.10000 REMARK 3 B22 (A**2) : -0.45000 REMARK 3 B33 (A**2) : 0.21000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.78000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.082 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.080 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.052 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.501 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6192 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 4095 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8420 ; 1.437 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9945 ; 1.311 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 782 ; 5.892 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 282 ;28.539 ;23.262 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 926 ;12.160 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 55 ;20.618 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 934 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6987 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1242 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1356 ; 0.215 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4598 ; 0.209 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3017 ; 0.172 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 3037 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 743 ; 0.125 ; 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): 15 ; 0.123 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 67 ; 0.343 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 68 ; 0.133 ; 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): 5041 ; 0.993 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6182 ; 1.050 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2600 ; 1.975 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2238 ; 2.843 ; 4.500 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 : 1.20 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 2VVP 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_1290036515. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-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 : ID14-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.931 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 115358 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.29000 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 (%): 56.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3000, 0.1 M TRIS PH 7, 0.2 M REMARK 280 CA ACETATE 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 68.41600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.52900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 68.41600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 51.52900 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: 4960 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: 5220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.5 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: 5290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.7 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 130.13675 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 69.40582 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 A2078 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 GLY B 159 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 PRO C 161 REMARK 465 ALA C 162 REMARK 465 MET D 1 REMARK 465 GLY D 159 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 PRO E 161 REMARK 465 ALA E 162 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 B 100 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 GLN B 139 CA - CB - CG ANGL. DEV. = 13.8 DEGREES 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 A2019 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A2020 DISTANCE = 7.75 ANGSTROMS REMARK 525 HOH E2010 DISTANCE = 5.95 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE R52 A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5RP A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE R52 B 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5RP B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE R52 C 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5RP C 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE R52 D 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5RP D 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE R52 E 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5RP E 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VVQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS RIBOSE-5-PHOSPHATE REMARK 900 ISOMERASE B IN COMPLEX WITH THE INHIBITOR 5-DEOXY-5-PHOSPHO-D- REMARK 900 RIBONATE 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: 2VVR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE H99N MUTANT OF RIBOSE-5-PHOSPHATE REMARK 900 ISOMERASE B FROM E. COLI 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 DBREF 2VVP A 1 162 UNP Q79FD7 RPIB_MYCTU 1 162 DBREF 2VVP B 1 162 UNP Q79FD7 RPIB_MYCTU 1 162 DBREF 2VVP C 1 162 UNP Q79FD7 RPIB_MYCTU 1 162 DBREF 2VVP D 1 162 UNP Q79FD7 RPIB_MYCTU 1 162 DBREF 2VVP 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 R52 A 200 14 HET 5RP A 300 14 HET R52 B 200 14 HET 5RP B 300 14 HET R52 C 200 14 HET 5RP C 300 14 HET R52 D 200 14 HET 5RP D 300 14 HET R52 E 200 14 HET 5RP E 300 14 HETNAM R52 5-O-PHOSPHONO-D-RIBOSE HETNAM 5RP RIBULOSE-5-PHOSPHATE FORMUL 6 R52 5(C5 H11 O8 P) FORMUL 7 5RP 5(C5 H11 O8 P) FORMUL 16 HOH *981(H2 O) HELIX 1 1 ASP A 11 THR A 28 1 18 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 ARG A 113 HIS A 115 5 3 HELIX 6 6 THR A 116 THR A 130 1 15 HELIX 7 7 ALA A 135 HIS A 152 1 18 HELIX 8 8 ASP B 11 THR B 28 1 18 HELIX 9 9 TYR B 46 ALA B 59 1 14 HELIX 10 10 GLY B 72 LYS B 81 1 10 HELIX 11 11 SER B 92 HIS B 102 1 11 HELIX 12 12 THR B 116 THR B 130 1 15 HELIX 13 13 ALA B 135 HIS B 152 1 18 HELIX 14 14 ASP C 11 THR C 28 1 18 HELIX 15 15 TYR C 46 ASP C 60 1 15 HELIX 16 16 GLY C 72 LYS C 81 1 10 HELIX 17 17 SER C 92 HIS C 102 1 11 HELIX 18 18 THR C 116 THR C 130 1 15 HELIX 19 19 ALA C 135 HIS C 152 1 18 HELIX 20 20 ASP D 11 THR D 28 1 18 HELIX 21 21 TYR D 46 ASP D 60 1 15 HELIX 22 22 GLY D 72 LYS D 81 1 10 HELIX 23 23 SER D 92 HIS D 102 1 11 HELIX 24 24 THR D 116 THR D 130 1 15 HELIX 25 25 ALA D 135 HIS D 152 1 18 HELIX 26 26 ASP E 11 THR E 28 1 18 HELIX 27 27 TYR E 46 ALA E 59 1 14 HELIX 28 28 GLY E 72 LYS E 81 1 10 HELIX 29 29 SER E 92 HIS E 102 1 11 HELIX 30 30 THR E 116 THR E 130 1 15 HELIX 31 31 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 36 ALA A 37 0 4.01 CISPEP 2 GLY B 36 ALA B 37 0 6.89 CISPEP 3 GLY C 36 ALA C 37 0 4.30 CISPEP 4 GLY D 36 ALA D 37 0 7.23 CISPEP 5 GLY E 36 ALA E 37 0 4.22 SITE 1 AC1 18 ASP A 11 HIS A 12 ALA A 13 GLY A 69 SITE 2 AC1 18 GLY A 70 SER A 71 GLY A 74 GLU A 75 SITE 3 AC1 18 ARG A 113 HOH A2188 HOH A2189 HOH A2190 SITE 4 AC1 18 HOH A2191 HOH A2192 HIS B 102 ASN B 103 SITE 5 AC1 18 ARG B 137 ARG B 141 SITE 1 AC2 17 ASP A 11 HIS A 12 GLY A 70 SER A 71 SITE 2 AC2 17 GLY A 72 ASN A 73 GLY A 74 GLU A 75 SITE 3 AC2 17 ARG A 113 HOH A2188 HOH A2190 HOH A2191 SITE 4 AC2 17 HOH A2192 HIS B 102 ASN B 103 ARG B 137 SITE 5 AC2 17 ARG B 141 SITE 1 AC3 18 HIS A 102 ASN A 103 ARG A 137 ARG A 141 SITE 2 AC3 18 ASP B 11 HIS B 12 ALA B 13 GLY B 69 SITE 3 AC3 18 GLY B 70 SER B 71 GLY B 74 GLU B 75 SITE 4 AC3 18 ARG B 113 HOH B2197 HOH B2198 HOH B2199 SITE 5 AC3 18 HOH B2200 HOH B2201 SITE 1 AC4 18 HIS A 102 ASN A 103 ARG A 137 ARG A 141 SITE 2 AC4 18 ASP B 11 HIS B 12 ALA B 13 GLY B 69 SITE 3 AC4 18 GLY B 70 SER B 71 ASN B 73 GLY B 74 SITE 4 AC4 18 GLU B 75 ARG B 113 HOH B2197 HOH B2198 SITE 5 AC4 18 HOH B2200 HOH B2201 SITE 1 AC5 17 ASP C 11 HIS C 12 ALA C 13 GLY C 70 SITE 2 AC5 17 SER C 71 GLY C 74 GLU C 75 ARG C 113 SITE 3 AC5 17 HOH C2202 HOH C2203 HOH C2204 HOH C2205 SITE 4 AC5 17 HOH C2206 HIS D 102 ASN D 103 ARG D 137 SITE 5 AC5 17 ARG D 141 SITE 1 AC6 19 ASP C 11 HIS C 12 ALA C 13 GLY C 69 SITE 2 AC6 19 GLY C 70 SER C 71 GLY C 72 ASN C 73 SITE 3 AC6 19 GLY C 74 GLU C 75 ARG C 113 HOH C2202 SITE 4 AC6 19 HOH C2203 HOH C2205 HOH C2206 HIS D 102 SITE 5 AC6 19 ASN D 103 ARG D 137 ARG D 141 SITE 1 AC7 17 HIS C 102 ASN C 103 ARG C 137 ARG C 141 SITE 2 AC7 17 ASP D 11 HIS D 12 ALA D 13 GLY D 69 SITE 3 AC7 17 GLY D 70 SER D 71 GLY D 74 GLU D 75 SITE 4 AC7 17 ARG D 113 HOH D2199 HOH D2200 HOH D2201 SITE 5 AC7 17 HOH D2202 SITE 1 AC8 16 HIS C 102 ASN C 103 ARG C 137 ARG C 141 SITE 2 AC8 16 ASP D 11 HIS D 12 ALA D 13 GLY D 70 SITE 3 AC8 16 SER D 71 GLY D 74 GLU D 75 ARG D 113 SITE 4 AC8 16 HOH D2199 HOH D2201 HOH D2202 HOH D2203 SITE 1 AC9 19 HOH D2158 ASP E 11 HIS E 12 ALA E 13 SITE 2 AC9 19 GLY E 69 GLY E 70 SER E 71 ASN E 73 SITE 3 AC9 19 GLY E 74 GLU E 75 HIS E 102 ASN E 103 SITE 4 AC9 19 ARG E 113 ARG E 137 ARG E 141 HOH E2177 SITE 5 AC9 19 HOH E2178 HOH E2179 HOH E2180 SITE 1 BC1 16 HOH D2158 ASP E 11 HIS E 12 ALA E 13 SITE 2 BC1 16 GLY E 70 SER E 71 GLY E 74 GLU E 75 SITE 3 BC1 16 HIS E 102 ASN E 103 ARG E 113 ARG E 137 SITE 4 BC1 16 ARG E 141 HOH E2178 HOH E2179 HOH E2180 CRYST1 136.832 103.058 69.728 90.00 95.51 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 0.007308 0.000000 0.000705 0.00000 SCALE2 0.000000 0.009703 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014408 0.00000 MTRIX1 1 -0.397220 0.913590 0.087030 22.72341 1 MTRIX2 1 0.912810 0.383500 0.140380 -16.97616 1 MTRIX3 1 0.094870 0.135210 -0.986260 19.99602 1 MTRIX1 2 -0.353060 -0.924940 0.140830 39.06989 1 MTRIX2 2 -0.923950 0.321010 -0.208040 35.13174 1 MTRIX3 2 0.147220 -0.203570 -0.967930 50.42159 1 MTRIX1 3 -0.690300 -0.659190 -0.298250 49.54621 1 MTRIX2 3 0.642460 -0.748050 0.166350 4.54831 1 MTRIX3 3 -0.332760 -0.076780 0.939880 37.83466 1 MTRIX1 4 -0.765120 0.538760 -0.352610 81.86645 1 MTRIX2 4 -0.547070 -0.832730 -0.085270 5.33485 1 MTRIX3 4 -0.339570 0.127660 0.931880 30.31059 1