HEADER ISOMERASE 10-JUN-03 1PM7 TITLE RMLC (DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE)STRUCTURE FROM TITLE 2 MYCOBACTERIUM TUBERCULOSIS AND INHIBITOR DESIGN. THE APO STRUCTURE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RFBC; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE, DTDP-6-DEOXY-D-XYLO-4- COMPND 5 HEXULOSE 3,5-EPIMERASE; COMPND 6 EC: 5.1.3.13; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: RMLC (RFBC); SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET23B(+) KEYWDS RMLC, BETA BARREL, MAIN BETA SHEET STRUCTURE, STRUCTURAL GENOMICS, KEYWDS 2 PSI, PROTEIN STRUCTURE INITIATIVE, TB STRUCTURAL GENOMICS KEYWDS 3 CONSORTIUM, TBSGC, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.DONG,J.H.NAISMITH,TB STRUCTURAL GENOMICS CONSORTIUM (TBSGC) REVDAT 7 14-FEB-24 1PM7 1 REMARK REVDAT 6 13-JUL-11 1PM7 1 VERSN REVDAT 5 24-FEB-09 1PM7 1 VERSN REVDAT 4 01-FEB-05 1PM7 1 AUTHOR KEYWDS REMARK REVDAT 3 25-JAN-05 1PM7 1 JRNL REVDAT 2 22-JUN-04 1PM7 1 DBREF REVDAT 1 09-DEC-03 1PM7 0 JRNL AUTH K.BABAOGLU,M.A.PAGE,V.C.JONES,M.R.MCNEIL,C.DONG, JRNL AUTH 2 J.H.NAISMITH,R.E.LEE JRNL TITL NOVEL INHIBITORS OF AN EMERGING TARGET IN MYCOBACTERIUM JRNL TITL 2 TUBERCULOSIS; SUBSTITUTED THIAZOLIDINONES AS INHIBITORS OF JRNL TITL 3 DTDP-RHAMNOSE SYNTHESIS. JRNL REF BIOORG.MED.CHEM.LETT. V. 13 3227 2003 JRNL REFN ISSN 0960-894X JRNL PMID 12951098 JRNL DOI 10.1016/S0960-894X(03)00673-5 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 20551 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1110 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1511 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE SET COUNT : 84 REMARK 3 BIN FREE R VALUE : 0.3410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3100 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 155 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.74000 REMARK 3 B22 (A**2) : 0.74000 REMARK 3 B33 (A**2) : -1.12000 REMARK 3 B12 (A**2) : 0.37000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.254 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.229 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.261 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3196 ; 0.017 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2826 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4352 ; 1.682 ; 1.934 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6538 ; 0.905 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 396 ; 9.212 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 476 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3622 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 692 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 656 ; 0.219 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3305 ; 0.254 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1934 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 141 ; 0.192 ; 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): 27 ; 0.291 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 74 ; 0.284 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.191 ; 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): 1988 ; 0.690 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3198 ; 1.062 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1208 ; 1.656 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1154 ; 2.331 ; 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): 3196 ; 1.027 ; 2.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 167 ; 3.472 ; 2.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3120 ; 1.401 ; 2.000 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 199 REMARK 3 ORIGIN FOR THE GROUP (A): 22.3491 28.4717 -1.4320 REMARK 3 T TENSOR REMARK 3 T11: 0.2207 T22: 0.3500 REMARK 3 T33: 0.1500 T12: -0.2564 REMARK 3 T13: 0.0511 T23: -0.0346 REMARK 3 L TENSOR REMARK 3 L11: 6.2716 L22: 2.9388 REMARK 3 L33: 5.3026 L12: 2.3505 REMARK 3 L13: 0.7939 L23: -0.9692 REMARK 3 S TENSOR REMARK 3 S11: 0.2171 S12: 0.4153 S13: 0.0691 REMARK 3 S21: 0.3070 S22: 0.0011 S23: -0.0850 REMARK 3 S31: -0.8219 S32: 1.0970 S33: -0.2181 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 199 REMARK 3 ORIGIN FOR THE GROUP (A): -2.7644 13.9892 1.5680 REMARK 3 T TENSOR REMARK 3 T11: 0.0831 T22: 0.4623 REMARK 3 T33: 0.1497 T12: -0.1732 REMARK 3 T13: 0.0011 T23: 0.0484 REMARK 3 L TENSOR REMARK 3 L11: 5.5726 L22: 3.9244 REMARK 3 L33: 5.1948 L12: 2.6665 REMARK 3 L13: -0.6138 L23: 1.1295 REMARK 3 S TENSOR REMARK 3 S11: 0.3337 S12: 0.1962 S13: -0.0466 REMARK 3 S21: 0.3198 S22: -0.1434 S23: 0.0803 REMARK 3 S31: 0.5249 S32: -1.2481 S33: -0.1903 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1PM7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-03. REMARK 100 THE DEPOSITION ID IS D_1000019422. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-APR-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 1.448 REMARK 200 MONOCHROMATOR : LIQUID GALLIUM COOLED, BENT, REMARK 200 TRIANGULARY SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21690 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 56.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 11.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : 0.04400 REMARK 200 FOR THE DATA SET : 1.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.42300 REMARK 200 R SYM FOR SHELL (I) : 0.36400 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8K, 0.2M CALCIUM ACETATE, 0.1M REMARK 280 SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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 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 58.41333 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 29.20667 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 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: 3890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 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 ARG A 200 REMARK 465 GLY A 201 REMARK 465 THR A 202 REMARK 465 ARG B 200 REMARK 465 GLY B 201 REMARK 465 THR B 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 NZ LYS B 2 O HOH B 322 1.95 REMARK 500 O ILE B 196 O GLU B 198 1.96 REMARK 500 N MET B 1 O THR B 15 1.98 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 GLU A 143 CD GLU A 143 OE2 0.072 REMARK 500 MET B 1 N MET B 1 CA 0.298 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 PRO A 67 C - N - CA ANGL. DEV. = 9.5 DEGREES REMARK 500 ASP A 107 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 169 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 MET B 1 N - CA - CB ANGL. DEV. = 14.5 DEGREES REMARK 500 ASP B 44 CB - CG - OD1 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP B 44 CB - CG - OD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 PRO B 68 C - N - CA ANGL. DEV. = 10.0 DEGREES REMARK 500 PRO B 68 N - CD - CG ANGL. DEV. = -9.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO A 67 108.11 13.79 REMARK 500 SER A 69 -163.09 54.37 REMARK 500 GLN A 106 -62.65 -101.58 REMARK 500 LEU A 159 48.02 -179.00 REMARK 500 PRO B 68 -39.21 2.03 REMARK 500 SER B 69 -163.61 48.39 REMARK 500 VAL B 160 -95.49 -68.84 REMARK 500 ASP B 161 47.50 -91.51 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 LEU A 66 PRO A 67 -112.51 REMARK 500 LEU A 159 VAL A 160 145.86 REMARK 500 PRO B 67 PRO B 68 -111.95 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 ACT A 260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 261 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 250 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 251 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: RV3465 RELATED DB: TARGETDB DBREF 1PM7 A 1 202 UNP O06330 O06330_MYCTU 1 202 DBREF 1PM7 B 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 HET ACT A 260 4 HET GOL A 250 6 HET ACT B 261 4 HET GOL B 251 6 HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ACT 2(C2 H3 O2 1-) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 7 HOH *155(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 ASN B 139 GLN B 141 5 3 HELIX 7 7 SER B 168 ALA B 173 1 6 HELIX 8 8 SER B 176 SER B 183 1 8 HELIX 9 9 ARG B 188 GLU B 198 1 11 SHEET 1 A 8 LYS A 2 GLU A 5 0 SHEET 2 A 8 ALA A 11 THR A 15 -1 O GLU A 13 N ARG A 4 SHEET 3 A 8 THR A 110 VAL A 113 -1 O THR A 110 N ILE A 14 SHEET 4 A 8 LYS A 72 SER A 78 -1 N LYS A 72 O VAL A 113 SHEET 5 A 8 SER A 128 CYS A 134 -1 O MET A 131 N THR A 75 SHEET 6 A 8 GLN A 47 SER A 53 -1 N SER A 51 O VAL A 130 SHEET 7 A 8 GLY B 24 THR B 31 -1 O PHE B 27 N CYS A 50 SHEET 8 A 8 HIS B 19 ASP B 21 -1 N ASP B 21 O GLY B 24 SHEET 1 B 8 HIS A 19 ASP A 21 0 SHEET 2 B 8 GLY A 24 THR A 31 -1 O GLY A 24 N ASP A 21 SHEET 3 B 8 GLN B 47 SER B 53 -1 O VAL B 48 N LEU A 30 SHEET 4 B 8 SER B 128 CYS B 134 -1 O CYS B 134 N GLN B 47 SHEET 5 B 8 LYS B 72 SER B 78 -1 N THR B 75 O MET B 131 SHEET 6 B 8 THR B 110 VAL B 113 -1 O VAL B 113 N LYS B 72 SHEET 7 B 8 ALA B 11 THR B 15 -1 N ILE B 14 O THR B 110 SHEET 8 B 8 LYS B 2 GLU B 5 -1 N ARG B 4 O GLU B 13 SHEET 1 C 5 TRP A 98 ASP A 104 0 SHEET 2 C 5 SER A 80 VAL A 86 -1 N ASP A 83 O VAL A 101 SHEET 3 C 5 ALA A 118 ALA A 123 -1 O GLY A 120 N VAL A 84 SHEET 4 C 5 LEU A 58 ALA A 64 -1 N HIS A 62 O HIS A 119 SHEET 5 C 5 GLU A 143 THR A 145 -1 O HIS A 144 N PHE A 63 SHEET 1 D 5 TRP B 98 ASP B 104 0 SHEET 2 D 5 SER B 80 VAL B 86 -1 N VAL B 81 O LEU B 103 SHEET 3 D 5 ALA B 118 ALA B 123 -1 O GLY B 120 N VAL B 84 SHEET 4 D 5 LEU B 58 ALA B 64 -1 N ARG B 59 O PHE B 121 SHEET 5 D 5 GLU B 143 THR B 145 -1 O HIS B 144 N PHE B 63 CISPEP 1 GLY A 60 LEU A 61 0 -5.52 CISPEP 2 PRO A 67 PRO A 68 0 -13.66 CISPEP 3 GLY B 60 LEU B 61 0 -2.33 SITE 1 AC1 3 HIS A 62 LYS A 72 HIS A 119 SITE 1 AC2 3 HIS B 62 LYS B 72 HIS B 119 SITE 1 AC3 4 MET A 1 LYS A 2 PRO A 16 THR A 17 SITE 1 AC4 10 MET B 1 PRO B 16 GLU B 28 TRP B 29 SITE 2 AC4 10 LEU B 30 GLY B 34 PHE B 35 TYR B 73 SITE 3 AC4 10 HOH B 265 HOH B 309 CRYST1 66.066 66.066 87.620 90.00 90.00 120.00 P 32 6 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 0.015136 0.008739 0.000000 0.00000 SCALE2 0.000000 0.017478 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011413 0.00000