HEADER ISOMERASE 07-JUL-06 2IXC TITLE RMLC M. TUBERCULOSIS WITH DTDP-RHAMNOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE RMLC; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: DTDP-4-KETO-6-DEOXYGLUCOSE 3,5-EPIMERASE, DTDP-L-RHAMNOSE COMPND 5 SYNTHETASE, THYMIDINE DIPHOSPHO-4-KETO-RHAMNOSE 3,5-EPIMERASE, DTDP- COMPND 6 4-DEHYDRORHAMNOSE 3,5-EPIMERASE; COMPND 7 EC: 5.1.3.13; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ISOMERASE, LIPOPOLYSACCHARIDE BIOSYNTHESIS, EPIMERISE, EPIMERASE, KEYWDS 2 EPIMERIZE EXPDTA X-RAY DIFFRACTION AUTHOR C.DONG,J.H.NAISMITH REVDAT 4 09-OCT-19 2IXC 1 REMARK REVDAT 3 24-FEB-09 2IXC 1 VERSN REVDAT 2 06-DEC-06 2IXC 1 JRNL REVDAT 1 26-OCT-06 2IXC 0 JRNL AUTH C.DONG,L.L.MAJOR,V.SRIKANNATHASAN,J.C.ERREY,M.F.GIRAUD, JRNL AUTH 2 J.S.LAM,M.GRANINGER,P.MESSNER,M.R.MCNEIL,R.A.FIELD, JRNL AUTH 3 C.WHITFIELD,J.H.NAISMITH JRNL TITL RMLC, A C3' AND C5' CARBOHYDRATE EPIMERASE, APPEARS TO JRNL TITL 2 OPERATE VIA AN INTERMEDIATE WITH AN UNUSUAL TWIST BOAT JRNL TITL 3 CONFORMATION. JRNL REF J.MOL.BIOL. V. 365 146 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17046787 JRNL DOI 10.1016/J.JMB.2006.09.063 REMARK 2 REMARK 2 RESOLUTION. 1.79 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) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 71906 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) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3784 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) : 1.79 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5105 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.01 REMARK 3 BIN R VALUE (WORKING SET) : 0.2070 REMARK 3 BIN FREE R VALUE SET COUNT : 242 REMARK 3 BIN FREE R VALUE : 0.2550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6172 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 140 REMARK 3 SOLVENT ATOMS : 1162 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.18000 REMARK 3 B22 (A**2) : 0.09000 REMARK 3 B33 (A**2) : 0.07000 REMARK 3 B12 (A**2) : 0.09000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : 0.04000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.360 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.118 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.077 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.449 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6480 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8868 ; 1.339 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 788 ; 5.713 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 308 ;33.436 ;23.117 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 940 ;12.295 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 56 ;16.951 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 988 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5024 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3079 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4373 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 1049 ; 0.156 ; 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): 57 ; 0.235 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 76 ; 0.169 ; 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): 4077 ; 0.864 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6364 ; 1.186 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2793 ; 1.828 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2504 ; 2.644 ; 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): 6870 ; 1.187 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 1163 ; 3.814 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6312 ; 1.757 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 3 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 5 A 190 4 REMARK 3 1 B 5 B 190 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 1441 ; 0.28 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1441 ; 0.53 ; 2.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A C REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 5 A 190 4 REMARK 3 1 C 5 C 190 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 A (A): 1441 ; 0.41 ; 0.50 REMARK 3 MEDIUM THERMAL 2 A (A**2): 1441 ; 0.73 ; 2.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 3 REMARK 3 CHAIN NAMES : A D REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 5 A 190 4 REMARK 3 1 D 5 D 190 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 3 A (A): 1441 ; 0.16 ; 0.50 REMARK 3 MEDIUM THERMAL 3 A (A**2): 1441 ; 0.53 ; 2.00 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 : 1.40 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 2IXC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-JUL-06. REMARK 100 THE DEPOSITION ID IS D_1290029307. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.488 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 : 84823 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 36.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23% (W/V) POLYETHYLENE GLYCOL (PEG) REMARK 280 8000, 0.2 M CALCIUM ACETATE HYDRATE, 0.1 M SODIUM CACODYLATE (PH REMARK 280 5.8) REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 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 199 REMARK 465 ARG A 200 REMARK 465 GLY A 201 REMARK 465 THR A 202 REMARK 465 MET B 199 REMARK 465 ARG B 200 REMARK 465 GLY B 201 REMARK 465 THR B 202 REMARK 465 MET C 199 REMARK 465 ARG C 200 REMARK 465 GLY C 201 REMARK 465 THR C 202 REMARK 465 MET D 199 REMARK 465 ARG D 200 REMARK 465 GLY D 201 REMARK 465 THR D 202 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH C 2189 O HOH C 2204 2.01 REMARK 500 O HOH C 2031 O HOH C 2080 2.02 REMARK 500 O HOH C 2309 O HOH C 2311 2.03 REMARK 500 O1P TRH B 1199 O HOH B 2295 2.04 REMARK 500 CB THR D 145 O HOH D 2200 2.13 REMARK 500 CG MET B 131 O HOH B 2115 2.15 REMARK 500 CE MET B 131 O HOH B 2115 2.17 REMARK 500 O HOH C 2059 O HOH C 2324 2.17 REMARK 500 O HOH A 2248 O HOH A 2250 2.18 REMARK 500 OE2 GLU B 178 O HOH B 2267 2.19 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 SER A 69 -152.54 52.32 REMARK 500 GLN A 106 -64.69 -101.86 REMARK 500 ASP A 161 58.53 -115.21 REMARK 500 SER B 69 -151.57 53.63 REMARK 500 GLN B 106 -66.58 -99.46 REMARK 500 SER C 69 -152.96 56.44 REMARK 500 SER D 69 -154.29 53.06 REMARK 500 GLN D 106 -61.58 -104.49 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 A2025 DISTANCE = 6.44 ANGSTROMS REMARK 525 HOH A2038 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH B2017 DISTANCE = 7.24 ANGSTROMS REMARK 525 HOH B2035 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH B2051 DISTANCE = 6.40 ANGSTROMS REMARK 525 HOH B2055 DISTANCE = 6.72 ANGSTROMS REMARK 525 HOH D2012 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH D2025 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH D2053 DISTANCE = 6.11 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRH A1199 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRH B1199 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRH C1199 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRH D1199 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PM7 RELATED DB: PDB REMARK 900 RMLC (DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3, 5-EPIMERASE)STRUCTURE FROM REMARK 900 MYCOBACTERIUM TUBERCULOSIS AND INHIBITORDESIGN. THE APO STRUCTURE. REMARK 900 RELATED ID: 1UPI RELATED DB: PDB REMARK 900 MYCOBACTERIUM TUBERCULOSIS RMLC EPIMERASE ( RV3465) REMARK 900 RELATED ID: 2IXH RELATED DB: PDB REMARK 900 RMLC P AUERGINOSA WITHG DTDP-RHAMNOSE REMARK 900 RELATED ID: 2IXI RELATED DB: PDB REMARK 900 RMLC P AUERGINOSA WITHG DTDP-XYLOSE REMARK 900 RELATED ID: 2IXJ RELATED DB: PDB REMARK 900 RMLC P AUERGINOSA NATIVE REMARK 900 RELATED ID: 2IXK RELATED DB: PDB REMARK 900 RMLC P AUERGINOSA WITHG DTDP-4-KETO RHAMNNOSE (THE PRODUCT OF THE REMARK 900 REACTION) REMARK 900 RELATED ID: 2IXL RELATED DB: PDB REMARK 900 RMLC S. SUIS WITH DTDP-RHAMNOSE DBREF 2IXC A 1 202 UNP O06330 O06330_MYCTU 1 202 DBREF 2IXC B 1 202 UNP O06330 O06330_MYCTU 1 202 DBREF 2IXC C 1 202 UNP O06330 O06330_MYCTU 1 202 DBREF 2IXC D 1 202 UNP O06330 O06330_MYCTU 1 202 SEQRES 1 A 202 MET LYS ALA ARG GLU LEU ASP VAL PRO GLY ALA TRP GLU SEQRES 2 A 202 ILE THR PRO THR ILE HIS VAL ASP SER ARG GLY LEU PHE SEQRES 3 A 202 PHE GLU TRP LEU THR ASP HIS GLY PHE ARG ALA PHE ALA SEQRES 4 A 202 GLY HIS SER LEU ASP VAL ARG GLN VAL ASN CYS SER VAL SEQRES 5 A 202 SER SER ALA GLY VAL LEU ARG GLY LEU HIS PHE ALA GLN SEQRES 6 A 202 LEU PRO PRO SER GLN ALA LYS TYR VAL THR CYS VAL SER SEQRES 7 A 202 GLY SER VAL PHE ASP VAL VAL VAL ASP ILE ARG GLU GLY SEQRES 8 A 202 SER PRO THR PHE GLY ARG TRP ASP SER VAL LEU LEU ASP SEQRES 9 A 202 ASP GLN ASP ARG ARG THR ILE TYR VAL SER GLU GLY LEU SEQRES 10 A 202 ALA HIS GLY PHE LEU ALA LEU GLN ASP ASN SER THR VAL SEQRES 11 A 202 MET TYR LEU CYS SER ALA GLU TYR ASN PRO GLN ARG GLU SEQRES 12 A 202 HIS THR ILE CYS ALA THR ASP PRO THR LEU ALA VAL ASP SEQRES 13 A 202 TRP PRO LEU VAL ASP GLY ALA ALA PRO SER LEU SER ASP SEQRES 14 A 202 ARG ASP ALA ALA ALA PRO SER PHE GLU ASP VAL ARG ALA SEQRES 15 A 202 SER GLY LEU LEU PRO ARG TRP GLU GLN THR GLN ARG PHE SEQRES 16 A 202 ILE GLY GLU MET ARG GLY THR SEQRES 1 B 202 MET LYS ALA ARG GLU LEU ASP VAL PRO GLY ALA TRP GLU SEQRES 2 B 202 ILE THR PRO THR ILE HIS VAL ASP SER ARG GLY LEU PHE SEQRES 3 B 202 PHE GLU TRP LEU THR ASP HIS GLY PHE ARG ALA PHE ALA SEQRES 4 B 202 GLY HIS SER LEU ASP VAL ARG GLN VAL ASN CYS SER VAL SEQRES 5 B 202 SER SER ALA GLY VAL LEU ARG GLY LEU HIS PHE ALA GLN SEQRES 6 B 202 LEU PRO PRO SER GLN ALA LYS TYR VAL THR CYS VAL SER SEQRES 7 B 202 GLY SER VAL PHE ASP VAL VAL VAL ASP ILE ARG GLU GLY SEQRES 8 B 202 SER PRO THR PHE GLY ARG TRP ASP SER VAL LEU LEU ASP SEQRES 9 B 202 ASP GLN ASP ARG ARG THR ILE TYR VAL SER GLU GLY LEU SEQRES 10 B 202 ALA HIS GLY PHE LEU ALA LEU GLN ASP ASN SER THR VAL SEQRES 11 B 202 MET TYR LEU CYS SER ALA GLU TYR ASN PRO GLN ARG GLU SEQRES 12 B 202 HIS THR ILE CYS ALA THR ASP PRO THR LEU ALA VAL ASP SEQRES 13 B 202 TRP PRO LEU VAL ASP GLY ALA ALA PRO SER LEU SER ASP SEQRES 14 B 202 ARG ASP ALA ALA ALA PRO SER PHE GLU ASP VAL ARG ALA SEQRES 15 B 202 SER GLY LEU LEU PRO ARG TRP GLU GLN THR GLN ARG PHE SEQRES 16 B 202 ILE GLY GLU MET ARG GLY THR SEQRES 1 C 202 MET LYS ALA ARG GLU LEU ASP VAL PRO GLY ALA TRP GLU SEQRES 2 C 202 ILE THR PRO THR ILE HIS VAL ASP SER ARG GLY LEU PHE SEQRES 3 C 202 PHE GLU TRP LEU THR ASP HIS GLY PHE ARG ALA PHE ALA SEQRES 4 C 202 GLY HIS SER LEU ASP VAL ARG GLN VAL ASN CYS SER VAL SEQRES 5 C 202 SER SER ALA GLY VAL LEU ARG GLY LEU HIS PHE ALA GLN SEQRES 6 C 202 LEU PRO PRO SER GLN ALA LYS TYR VAL THR CYS VAL SER SEQRES 7 C 202 GLY SER VAL PHE ASP VAL VAL VAL ASP ILE ARG GLU GLY SEQRES 8 C 202 SER PRO THR PHE GLY ARG TRP ASP SER VAL LEU LEU ASP SEQRES 9 C 202 ASP GLN ASP ARG ARG THR ILE TYR VAL SER GLU GLY LEU SEQRES 10 C 202 ALA HIS GLY PHE LEU ALA LEU GLN ASP ASN SER THR VAL SEQRES 11 C 202 MET TYR LEU CYS SER ALA GLU TYR ASN PRO GLN ARG GLU SEQRES 12 C 202 HIS THR ILE CYS ALA THR ASP PRO THR LEU ALA VAL ASP SEQRES 13 C 202 TRP PRO LEU VAL ASP GLY ALA ALA PRO SER LEU SER ASP SEQRES 14 C 202 ARG ASP ALA ALA ALA PRO SER PHE GLU ASP VAL ARG ALA SEQRES 15 C 202 SER GLY LEU LEU PRO ARG TRP GLU GLN THR GLN ARG PHE SEQRES 16 C 202 ILE GLY GLU MET ARG GLY THR SEQRES 1 D 202 MET LYS ALA ARG GLU LEU ASP VAL PRO GLY ALA TRP GLU SEQRES 2 D 202 ILE THR PRO THR ILE HIS VAL ASP SER ARG GLY LEU PHE SEQRES 3 D 202 PHE GLU TRP LEU THR ASP HIS GLY PHE ARG ALA PHE ALA SEQRES 4 D 202 GLY HIS SER LEU ASP VAL ARG GLN VAL ASN CYS SER VAL SEQRES 5 D 202 SER SER ALA GLY VAL LEU ARG GLY LEU HIS PHE ALA GLN SEQRES 6 D 202 LEU PRO PRO SER GLN ALA LYS TYR VAL THR CYS VAL SER SEQRES 7 D 202 GLY SER VAL PHE ASP VAL VAL VAL ASP ILE ARG GLU GLY SEQRES 8 D 202 SER PRO THR PHE GLY ARG TRP ASP SER VAL LEU LEU ASP SEQRES 9 D 202 ASP GLN ASP ARG ARG THR ILE TYR VAL SER GLU GLY LEU SEQRES 10 D 202 ALA HIS GLY PHE LEU ALA LEU GLN ASP ASN SER THR VAL SEQRES 11 D 202 MET TYR LEU CYS SER ALA GLU TYR ASN PRO GLN ARG GLU SEQRES 12 D 202 HIS THR ILE CYS ALA THR ASP PRO THR LEU ALA VAL ASP SEQRES 13 D 202 TRP PRO LEU VAL ASP GLY ALA ALA PRO SER LEU SER ASP SEQRES 14 D 202 ARG ASP ALA ALA ALA PRO SER PHE GLU ASP VAL ARG ALA SEQRES 15 D 202 SER GLY LEU LEU PRO ARG TRP GLU GLN THR GLN ARG PHE SEQRES 16 D 202 ILE GLY GLU MET ARG GLY THR HET TRH A1199 35 HET TRH B1199 35 HET TRH C1199 35 HET TRH D1199 35 HETNAM TRH 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE FORMUL 5 TRH 4(C16 H26 N2 O15 P2) FORMUL 9 HOH *1162(H2 O) HELIX 1 1 ASP A 32 GLY A 40 1 9 HELIX 2 2 SER A 168 ALA A 173 1 6 HELIX 3 3 SER A 176 SER A 183 1 8 HELIX 4 4 ARG A 188 GLU A 198 1 11 HELIX 5 5 ASP B 32 GLY B 40 1 9 HELIX 6 6 LEU B 159 ALA B 163 5 5 HELIX 7 7 SER B 168 ALA B 173 1 6 HELIX 8 8 SER B 176 GLY B 184 1 9 HELIX 9 9 ARG B 188 GLU B 198 1 11 HELIX 10 10 ASP C 32 GLY C 40 1 9 HELIX 11 11 SER C 168 ALA C 173 1 6 HELIX 12 12 SER C 176 GLY C 184 1 9 HELIX 13 13 ARG C 188 GLU C 198 1 11 HELIX 14 14 ASP D 32 GLY D 40 1 9 HELIX 15 15 LEU D 159 ALA D 163 5 5 HELIX 16 16 SER D 168 ALA D 173 1 6 HELIX 17 17 SER D 176 SER D 183 1 8 HELIX 18 18 ARG D 188 GLU D 198 1 11 SHEET 1 AA 8 LYS A 2 GLU A 5 0 SHEET 2 AA 8 ALA A 11 THR A 15 -1 O GLU A 13 N ARG A 4 SHEET 3 AA 8 THR A 110 VAL A 113 -1 O THR A 110 N ILE A 14 SHEET 4 AA 8 LYS A 72 SER A 78 -1 O LYS A 72 N VAL A 113 SHEET 5 AA 8 SER A 128 CYS A 134 -1 O THR A 129 N VAL A 77 SHEET 6 AA 8 GLN A 47 SER A 53 -1 O GLN A 47 N CYS A 134 SHEET 7 AA 8 GLY B 24 THR B 31 -1 O LEU B 25 N VAL A 52 SHEET 8 AA 8 HIS B 19 ASP B 21 -1 O HIS B 19 N PHE B 26 SHEET 1 AB 8 HIS A 19 ASP A 21 0 SHEET 2 AB 8 GLY A 24 THR A 31 -1 O GLY A 24 N ASP A 21 SHEET 3 AB 8 GLN B 47 SER B 53 -1 O VAL B 48 N TRP A 29 SHEET 4 AB 8 SER B 128 CYS B 134 -1 O SER B 128 N SER B 53 SHEET 5 AB 8 LYS B 72 SER B 78 -1 O TYR B 73 N LEU B 133 SHEET 6 AB 8 THR B 110 VAL B 113 -1 O ILE B 111 N VAL B 74 SHEET 7 AB 8 ALA B 11 THR B 15 -1 O TRP B 12 N TYR B 112 SHEET 8 AB 8 LYS B 2 GLU B 5 -1 O LYS B 2 N THR B 15 SHEET 1 AC 5 TRP A 98 ASP A 104 0 SHEET 2 AC 5 SER A 80 VAL A 86 -1 O VAL A 81 N LEU A 103 SHEET 3 AC 5 ALA A 118 ALA A 123 -1 O ALA A 118 N VAL A 86 SHEET 4 AC 5 LEU A 58 ALA A 64 -1 O ARG A 59 N PHE A 121 SHEET 5 AC 5 GLU A 143 THR A 145 -1 O HIS A 144 N PHE A 63 SHEET 1 BA 5 TRP B 98 ASP B 104 0 SHEET 2 BA 5 SER B 80 VAL B 86 -1 O VAL B 81 N LEU B 103 SHEET 3 BA 5 ALA B 118 ALA B 123 -1 O ALA B 118 N VAL B 86 SHEET 4 BA 5 LEU B 58 ALA B 64 -1 O ARG B 59 N PHE B 121 SHEET 5 BA 5 GLU B 143 THR B 145 -1 O HIS B 144 N PHE B 63 SHEET 1 CA 8 LYS C 2 GLU C 5 0 SHEET 2 CA 8 ALA C 11 THR C 15 -1 O GLU C 13 N ARG C 4 SHEET 3 CA 8 THR C 110 VAL C 113 -1 O THR C 110 N ILE C 14 SHEET 4 CA 8 LYS C 72 SER C 78 -1 O LYS C 72 N VAL C 113 SHEET 5 CA 8 SER C 128 CYS C 134 -1 O THR C 129 N VAL C 77 SHEET 6 CA 8 GLN C 47 SER C 53 -1 O GLN C 47 N CYS C 134 SHEET 7 CA 8 GLY D 24 THR D 31 -1 O LEU D 25 N VAL C 52 SHEET 8 CA 8 HIS D 19 ASP D 21 -1 O HIS D 19 N PHE D 26 SHEET 1 CB 8 ILE C 18 ASP C 21 0 SHEET 2 CB 8 GLY C 24 THR C 31 -1 O GLY C 24 N ASP C 21 SHEET 3 CB 8 GLN D 47 SER D 53 -1 O VAL D 48 N TRP C 29 SHEET 4 CB 8 SER D 128 CYS D 134 -1 O SER D 128 N SER D 53 SHEET 5 CB 8 LYS D 72 SER D 78 -1 O TYR D 73 N LEU D 133 SHEET 6 CB 8 THR D 110 VAL D 113 -1 O ILE D 111 N VAL D 74 SHEET 7 CB 8 ALA D 11 THR D 15 -1 O TRP D 12 N TYR D 112 SHEET 8 CB 8 LYS D 2 GLU D 5 -1 O LYS D 2 N THR D 15 SHEET 1 CC 5 TRP C 98 ASP C 104 0 SHEET 2 CC 5 SER C 80 VAL C 86 -1 O VAL C 81 N LEU C 103 SHEET 3 CC 5 ALA C 118 ALA C 123 -1 O ALA C 118 N VAL C 86 SHEET 4 CC 5 LEU C 58 ALA C 64 -1 O ARG C 59 N PHE C 121 SHEET 5 CC 5 GLU C 143 THR C 145 -1 O HIS C 144 N PHE C 63 SHEET 1 DA 5 TRP D 98 ASP D 104 0 SHEET 2 DA 5 SER D 80 VAL D 86 -1 O VAL D 81 N LEU D 103 SHEET 3 DA 5 ALA D 118 ALA D 123 -1 O ALA D 118 N VAL D 86 SHEET 4 DA 5 LEU D 58 ALA D 64 -1 O ARG D 59 N PHE D 121 SHEET 5 DA 5 GLU D 143 THR D 145 -1 O HIS D 144 N PHE D 63 CISPEP 1 GLY A 60 LEU A 61 0 -5.35 CISPEP 2 LEU A 66 PRO A 67 0 -2.71 CISPEP 3 PRO A 67 PRO A 68 0 -6.54 CISPEP 4 VAL A 160 ASP A 161 0 6.85 CISPEP 5 GLY B 60 LEU B 61 0 -5.97 CISPEP 6 LEU B 66 PRO B 67 0 -1.19 CISPEP 7 PRO B 67 PRO B 68 0 -5.30 CISPEP 8 GLY C 60 LEU C 61 0 -6.59 CISPEP 9 LEU C 66 PRO C 67 0 -4.99 CISPEP 10 PRO C 67 PRO C 68 0 -7.74 CISPEP 11 GLY D 60 LEU D 61 0 -6.57 CISPEP 12 LEU D 66 PRO D 67 0 -4.09 CISPEP 13 PRO D 67 PRO D 68 0 -7.17 SITE 1 AC1 23 GLN A 47 ASN A 49 ARG A 59 HIS A 62 SITE 2 AC1 23 LYS A 72 HIS A 119 TYR A 132 TYR A 138 SITE 3 AC1 23 ARG A 170 HOH A2218 HOH A2251 HOH A2252 SITE 4 AC1 23 HOH A2253 HOH A2254 HOH A2255 HOH A2256 SITE 5 AC1 23 HOH A2257 HIS B 19 ARG B 23 PHE B 26 SITE 6 AC1 23 GLU B 28 GLU C 90 ARG C 181 SITE 1 AC2 28 PHE A 26 GLU A 28 GLN B 47 ASN B 49 SITE 2 AC2 28 ARG B 59 HIS B 62 LYS B 72 HIS B 119 SITE 3 AC2 28 TYR B 132 TYR B 138 GLU B 143 ARG B 170 SITE 4 AC2 28 ASP B 171 HOH B2068 HOH B2220 HOH B2294 SITE 5 AC2 28 HOH B2295 HOH B2296 HOH B2297 HOH B2298 SITE 6 AC2 28 HOH B2299 HOH B2300 HOH B2301 HOH B2302 SITE 7 AC2 28 HOH B2303 HOH B2304 GLU D 90 ARG D 181 SITE 1 AC3 24 GLU A 90 ARG A 181 GLN C 47 ASN C 49 SITE 2 AC3 24 ARG C 59 HIS C 62 LYS C 72 HIS C 119 SITE 3 AC3 24 TYR C 132 TYR C 138 ARG C 170 HOH C2213 SITE 4 AC3 24 HOH C2317 HOH C2318 HOH C2319 HOH C2320 SITE 5 AC3 24 HOH C2321 HOH C2322 HOH C2323 HOH C2324 SITE 6 AC3 24 HOH C2326 HOH C2327 PHE D 26 GLU D 28 SITE 1 AC4 25 GLU B 90 ARG B 181 HIS C 19 ARG C 23 SITE 2 AC4 25 PHE C 26 GLU C 28 GLN D 47 ASN D 49 SITE 3 AC4 25 ARG D 59 HIS D 62 LYS D 72 HIS D 119 SITE 4 AC4 25 TYR D 132 TYR D 138 ARG D 170 HOH D2265 SITE 5 AC4 25 HOH D2266 HOH D2267 HOH D2268 HOH D2269 SITE 6 AC4 25 HOH D2270 HOH D2271 HOH D2272 HOH D2273 SITE 7 AC4 25 HOH D2274 CRYST1 44.778 56.845 90.700 89.90 78.28 82.33 P 1 4 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 0.022332 -0.003008 -0.004713 0.00000 SCALE2 0.000000 0.017751 0.000464 0.00000 SCALE3 0.000000 0.000000 0.011264 0.00000