HEADER LYASE 16-NOV-01 1KEP TITLE THE CRYSTAL STRUCTURE OF DTDP-D-GLUCOSE 4,6-DEHYDRATASE (RMLB) FROM TITLE 2 STREPTOCOCCUS SUIS WITH DTDP-XYLOSE BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: DTDP-D-GLUCOSE 4,6-DEHYDRATASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RMLB; COMPND 5 EC: 4.2.1.46; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS SUIS; SOURCE 3 ORGANISM_TAXID: 1307; SOURCE 4 VARIANT: SEROTYPE 2; SOURCE 5 GENE: RMLB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS ROSSMANN FOLD, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR S.T.M.ALLARD,K.BEIS,M.-F.GIRAUD,A.D.HEGEMAN,J.W.GROSS,C.WHITFIELD, AUTHOR 2 M.GRANINGER,P.MESSNER,A.G.ALLEN,J.H.NAISMITH REVDAT 5 16-AUG-23 1KEP 1 REMARK REVDAT 4 01-FEB-17 1KEP 1 AUTHOR VERSN REVDAT 3 24-FEB-09 1KEP 1 VERSN REVDAT 2 01-APR-03 1KEP 1 JRNL REVDAT 1 25-JAN-02 1KEP 0 JRNL AUTH S.T.ALLARD,K.BEIS,M.F.GIRAUD,A.D.HEGEMAN,J.W.GROSS, JRNL AUTH 2 R.C.WILMOUTH,C.WHITFIELD,M.GRANINGER,P.MESSNER,A.G.ALLEN, JRNL AUTH 3 D.J.MASKELL,J.H.NAISMITH JRNL TITL TOWARD A STRUCTURAL UNDERSTANDING OF THE DEHYDRATASE JRNL TITL 2 MECHANISM. JRNL REF STRUCTURE V. 10 81 2002 JRNL REFN ISSN 0969-2126 JRNL PMID 11796113 JRNL DOI 10.1016/S0969-2126(01)00694-3 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 91.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 91826 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) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 10151 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 591 REMARK 3 BIN FREE R VALUE : 0.2620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5478 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 149 REMARK 3 SOLVENT ATOMS : 804 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.82 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 6.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : 0.32000 REMARK 3 B33 (A**2) : -0.35000 REMARK 3 B12 (A**2) : 0.00000 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): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KEP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-NOV-01. REMARK 100 THE DEPOSITION ID IS D_1000014874. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.870 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MORRORS 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 : 91826 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 91.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : 0.07900 REMARK 200 FOR THE DATA SET : 6.9000 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 (%) : 85.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.36400 REMARK 200 R SYM FOR SHELL (I) : 0.29100 REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB 1G1A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% PEG 4000, 0.1M CITRIC ACID PH 5.4, REMARK 280 0.3M AMMONIUM SULPHATE AND 3% 1,6-HEXANEDIOL, VAPOR DIFFUSION, REMARK 280 HANGING DROP AT 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 31.22450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 92.73550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.59100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 92.73550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.22450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.59100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 7160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -83.0 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 MET A 1 REMARK 465 SER A 2 REMARK 465 MET B 1 REMARK 465 LYS B 348 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 ND2 ASN A 154 OD1 ASN B 154 1.47 REMARK 500 OD1 ASN A 19 O HOH A 6433 1.94 REMARK 500 OG SER B 2 O HOH B 6359 2.02 REMARK 500 O HOH A 6226 O HOH B 6358 2.03 REMARK 500 O HOH A 6100 O HOH A 6433 2.04 REMARK 500 OH TYR A 155 O HOH A 6164 2.19 REMARK 500 O HOH A 6065 O HOH A 6368 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 6295 O HOH A 6298 4556 2.17 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 ASP A 131 CA ASP A 131 CB 0.176 REMARK 500 ASP A 131 CB ASP A 131 CG -0.195 REMARK 500 SER A 163 CA SER A 163 CB 0.145 REMARK 500 GLN A 344 CB GLN A 344 CG -0.206 REMARK 500 ASP B 131 CB ASP B 131 CG -0.189 REMARK 500 GLU B 332 CD GLU B 332 OE2 0.077 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 ASP A 54 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP A 77 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 131 CB - CA - C ANGL. DEV. = -12.8 DEGREES REMARK 500 ASP A 131 CB - CG - OD1 ANGL. DEV. = -24.6 DEGREES REMARK 500 ASP A 131 CB - CG - OD2 ANGL. DEV. = 19.9 DEGREES REMARK 500 SER A 163 CA - CB - OG ANGL. DEV. = -26.3 DEGREES REMARK 500 ASP A 276 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP A 300 CB - CG - OD2 ANGL. DEV. = 8.7 DEGREES REMARK 500 ASP B 131 CB - CA - C ANGL. DEV. = -12.0 DEGREES REMARK 500 ASP B 131 CB - CG - OD1 ANGL. DEV. = -16.2 DEGREES REMARK 500 ASP B 131 CB - CG - OD2 ANGL. DEV. = 13.7 DEGREES REMARK 500 ASP B 300 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP B 310 CB - CG - OD2 ANGL. DEV. = 7.5 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 PHE A 15 -72.33 -67.75 REMARK 500 THR A 40 -172.43 -69.34 REMARK 500 PHE A 103 -60.46 -96.39 REMARK 500 ASN A 156 58.38 -163.75 REMARK 500 THR A 282 128.36 -37.70 REMARK 500 LEU A 289 -78.58 -72.71 REMARK 500 PHE A 308 70.56 -104.18 REMARK 500 THR B 40 -168.55 -72.75 REMARK 500 PHE B 103 -61.56 -97.66 REMARK 500 ASN B 156 59.41 -163.02 REMARK 500 THR B 282 124.23 -38.09 REMARK 500 HIS B 287 124.83 -37.51 REMARK 500 LEU B 289 -76.20 -71.39 REMARK 500 PHE B 308 71.66 -104.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 TDX A 3500 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 6001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 6002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 6003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 1400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 2400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TDX A 3500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TDX B 4500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KER RELATED DB: PDB REMARK 900 RMLB FROM STREPTOCOCCUS SUIS WITH DTDP-D-GLUCOSE BOUND REMARK 900 RELATED ID: 1KET RELATED DB: PDB REMARK 900 RMLB FROM STREPTOCOCCUS SUIS WITH THYMIDINE DIPHOSPHATE BOUND REMARK 900 RELATED ID: 1KEU RELATED DB: PDB REMARK 900 RMLB FROM SALMONELLA ENTERICA SEROVAR TYPHIMURIUM WITH DTDP-D- REMARK 900 GLUCOSE BOUND REMARK 900 RELATED ID: 1KEW RELATED DB: PDB REMARK 900 RMLB FROM SALMONELLA ENTERICA SEROVAR TYPHIMURIUM WITH NAD+ BOUND REMARK 900 RELATED ID: 1G1A RELATED DB: PDB REMARK 900 RMLB FROM SALMONELLA ENTERICA SEROVAR TYPHIMURIUM WITH NAD+ BOUND DBREF 1KEP A 5 344 UNP P95780 RMLB_STRMU 5 344 DBREF 1KEP B 5 344 UNP P95780 RMLB_STRMU 5 344 SEQRES 1 A 348 MET SER GLN PHE LYS ASN ILE ILE VAL THR GLY GLY ALA SEQRES 2 A 348 GLY PHE ILE GLY SER ASN PHE VAL HIS TYR VAL TYR ASN SEQRES 3 A 348 ASN HIS PRO ASP VAL HIS VAL THR VAL LEU ASP LYS LEU SEQRES 4 A 348 THR TYR ALA GLY ASN LYS ALA ASN LEU GLU ALA ILE LEU SEQRES 5 A 348 GLY ASP ARG VAL GLU LEU VAL VAL GLY ASP ILE ALA ASP SEQRES 6 A 348 ALA GLU LEU VAL ASP LYS LEU ALA ALA LYS ALA ASP ALA SEQRES 7 A 348 ILE VAL HIS TYR ALA ALA GLU SER HIS ASN ASP ASN SER SEQRES 8 A 348 LEU ASN ASP PRO SER PRO PHE ILE HIS THR ASN PHE ILE SEQRES 9 A 348 GLY THR TYR THR LEU LEU GLU ALA ALA ARG LYS TYR ASP SEQRES 10 A 348 ILE ARG PHE HIS HIS VAL SER THR ASP GLU VAL TYR GLY SEQRES 11 A 348 ASP LEU PRO LEU ARG GLU ASP LEU PRO GLY HIS GLY GLU SEQRES 12 A 348 GLY PRO GLY GLU LYS PHE THR ALA GLU THR ASN TYR ASN SEQRES 13 A 348 PRO SER SER PRO TYR SER SER THR LYS ALA ALA SER ASP SEQRES 14 A 348 LEU ILE VAL LYS ALA TRP VAL ARG SER PHE GLY VAL LYS SEQRES 15 A 348 ALA THR ILE SER ASN CYS SER ASN ASN TYR GLY PRO TYR SEQRES 16 A 348 GLN HIS ILE GLU LYS PHE ILE PRO ARG GLN ILE THR ASN SEQRES 17 A 348 ILE LEU ALA GLY ILE LYS PRO LYS LEU TYR GLY GLU GLY SEQRES 18 A 348 LYS ASN VAL ARG ASP TRP ILE HIS THR ASN ASP HIS SER SEQRES 19 A 348 THR GLY VAL TRP ALA ILE LEU THR LYS GLY ARG MET GLY SEQRES 20 A 348 GLU THR TYR LEU ILE GLY ALA ASP GLY GLU LYS ASN ASN SEQRES 21 A 348 LYS GLU VAL LEU GLU LEU ILE LEU GLU LYS MET GLY GLN SEQRES 22 A 348 PRO LYS ASP ALA TYR ASP HIS VAL THR ASP ARG ALA GLY SEQRES 23 A 348 HIS ASP LEU ARG TYR ALA ILE ASP ALA SER LYS LEU ARG SEQRES 24 A 348 ASP GLU LEU GLY TRP THR PRO GLN PHE THR ASP PHE SER SEQRES 25 A 348 GLU GLY LEU GLU GLU THR ILE GLN TRP TYR THR ASP ASN SEQRES 26 A 348 GLN ASP TRP TRP LYS ALA GLU LYS GLU ALA VAL GLU ALA SEQRES 27 A 348 ASN TYR ALA LYS THR GLN GLU VAL ILE LYS SEQRES 1 B 348 MET SER GLN PHE LYS ASN ILE ILE VAL THR GLY GLY ALA SEQRES 2 B 348 GLY PHE ILE GLY SER ASN PHE VAL HIS TYR VAL TYR ASN SEQRES 3 B 348 ASN HIS PRO ASP VAL HIS VAL THR VAL LEU ASP LYS LEU SEQRES 4 B 348 THR TYR ALA GLY ASN LYS ALA ASN LEU GLU ALA ILE LEU SEQRES 5 B 348 GLY ASP ARG VAL GLU LEU VAL VAL GLY ASP ILE ALA ASP SEQRES 6 B 348 ALA GLU LEU VAL ASP LYS LEU ALA ALA LYS ALA ASP ALA SEQRES 7 B 348 ILE VAL HIS TYR ALA ALA GLU SER HIS ASN ASP ASN SER SEQRES 8 B 348 LEU ASN ASP PRO SER PRO PHE ILE HIS THR ASN PHE ILE SEQRES 9 B 348 GLY THR TYR THR LEU LEU GLU ALA ALA ARG LYS TYR ASP SEQRES 10 B 348 ILE ARG PHE HIS HIS VAL SER THR ASP GLU VAL TYR GLY SEQRES 11 B 348 ASP LEU PRO LEU ARG GLU ASP LEU PRO GLY HIS GLY GLU SEQRES 12 B 348 GLY PRO GLY GLU LYS PHE THR ALA GLU THR ASN TYR ASN SEQRES 13 B 348 PRO SER SER PRO TYR SER SER THR LYS ALA ALA SER ASP SEQRES 14 B 348 LEU ILE VAL LYS ALA TRP VAL ARG SER PHE GLY VAL LYS SEQRES 15 B 348 ALA THR ILE SER ASN CYS SER ASN ASN TYR GLY PRO TYR SEQRES 16 B 348 GLN HIS ILE GLU LYS PHE ILE PRO ARG GLN ILE THR ASN SEQRES 17 B 348 ILE LEU ALA GLY ILE LYS PRO LYS LEU TYR GLY GLU GLY SEQRES 18 B 348 LYS ASN VAL ARG ASP TRP ILE HIS THR ASN ASP HIS SER SEQRES 19 B 348 THR GLY VAL TRP ALA ILE LEU THR LYS GLY ARG MET GLY SEQRES 20 B 348 GLU THR TYR LEU ILE GLY ALA ASP GLY GLU LYS ASN ASN SEQRES 21 B 348 LYS GLU VAL LEU GLU LEU ILE LEU GLU LYS MET GLY GLN SEQRES 22 B 348 PRO LYS ASP ALA TYR ASP HIS VAL THR ASP ARG ALA GLY SEQRES 23 B 348 HIS ASP LEU ARG TYR ALA ILE ASP ALA SER LYS LEU ARG SEQRES 24 B 348 ASP GLU LEU GLY TRP THR PRO GLN PHE THR ASP PHE SER SEQRES 25 B 348 GLU GLY LEU GLU GLU THR ILE GLN TRP TYR THR ASP ASN SEQRES 26 B 348 GLN ASP TRP TRP LYS ALA GLU LYS GLU ALA VAL GLU ALA SEQRES 27 B 348 ASN TYR ALA LYS THR GLN GLU VAL ILE LYS HET SO4 A6001 5 HET SO4 A6002 5 HET NAD A1400 44 HET TDX A3500 12 HET SO4 B6003 5 HET NAD B2400 44 HET TDX B4500 34 HETNAM SO4 SULFATE ION HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM TDX THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE FORMUL 3 SO4 3(O4 S 2-) FORMUL 5 NAD 2(C21 H27 N7 O14 P2) FORMUL 6 TDX 2(C15 H24 N2 O15 P2) FORMUL 10 HOH *804(H2 O) HELIX 1 1 GLY A 14 HIS A 28 1 15 HELIX 2 2 ASN A 44 LEU A 52 5 9 HELIX 3 3 ASP A 65 ALA A 74 1 10 HELIX 4 4 HIS A 87 ASP A 94 1 8 HELIX 5 5 PRO A 95 PHE A 103 1 9 HELIX 6 6 PHE A 103 ASP A 117 1 15 HELIX 7 7 GLU A 127 GLY A 130 5 4 HELIX 8 8 LEU A 134 LEU A 138 5 5 HELIX 9 9 SER A 159 GLY A 180 1 22 HELIX 10 10 LYS A 200 GLY A 212 1 13 HELIX 11 11 THR A 230 GLY A 244 1 15 HELIX 12 12 ASN A 260 MET A 271 1 12 HELIX 13 13 ALA A 295 GLY A 303 1 9 HELIX 14 14 ASP A 310 ASN A 325 1 16 HELIX 15 15 ASN A 325 LYS A 330 1 6 HELIX 16 16 GLU A 332 LYS A 342 1 11 HELIX 17 17 GLY B 14 HIS B 28 1 15 HELIX 18 18 ASN B 44 LEU B 52 5 9 HELIX 19 19 ASP B 65 ALA B 74 1 10 HELIX 20 20 HIS B 87 ASP B 94 1 8 HELIX 21 21 PRO B 95 PHE B 103 1 9 HELIX 22 22 PHE B 103 ASP B 117 1 15 HELIX 23 23 GLU B 127 GLY B 130 5 4 HELIX 24 24 LEU B 134 LEU B 138 5 5 HELIX 25 25 SER B 159 GLY B 180 1 22 HELIX 26 26 LYS B 200 GLY B 212 1 13 HELIX 27 27 THR B 230 GLY B 244 1 15 HELIX 28 28 ASN B 260 MET B 271 1 12 HELIX 29 29 ALA B 295 GLY B 303 1 9 HELIX 30 30 ASP B 310 ASN B 325 1 16 HELIX 31 31 ASN B 325 LYS B 330 1 6 HELIX 32 32 GLU B 332 LYS B 342 1 11 SHEET 1 A 7 VAL A 56 VAL A 60 0 SHEET 2 A 7 HIS A 32 ASP A 37 1 N VAL A 35 O VAL A 59 SHEET 3 A 7 ASN A 6 THR A 10 1 N ILE A 7 O THR A 34 SHEET 4 A 7 ALA A 78 HIS A 81 1 O VAL A 80 N ILE A 8 SHEET 5 A 7 ARG A 119 THR A 125 1 O HIS A 121 N HIS A 81 SHEET 6 A 7 ALA A 183 CYS A 188 1 O THR A 184 N HIS A 122 SHEET 7 A 7 THR A 249 ILE A 252 1 O TYR A 250 N ILE A 185 SHEET 1 B 2 ASN A 191 TYR A 192 0 SHEET 2 B 2 ILE A 228 HIS A 229 1 O ILE A 228 N TYR A 192 SHEET 1 C 2 LYS A 216 TYR A 218 0 SHEET 2 C 2 ASP A 279 VAL A 281 1 O ASP A 279 N LEU A 217 SHEET 1 D 2 VAL A 224 ASP A 226 0 SHEET 2 D 2 GLU A 257 ASN A 259 -1 O LYS A 258 N ARG A 225 SHEET 1 E 7 VAL B 56 VAL B 60 0 SHEET 2 E 7 HIS B 32 ASP B 37 1 N VAL B 35 O GLU B 57 SHEET 3 E 7 ASN B 6 THR B 10 1 N ILE B 7 O THR B 34 SHEET 4 E 7 ALA B 78 HIS B 81 1 O VAL B 80 N ILE B 8 SHEET 5 E 7 ARG B 119 THR B 125 1 O HIS B 121 N HIS B 81 SHEET 6 E 7 ALA B 183 CYS B 188 1 O THR B 184 N HIS B 122 SHEET 7 E 7 THR B 249 ILE B 252 1 O TYR B 250 N ILE B 185 SHEET 1 F 2 ASN B 191 TYR B 192 0 SHEET 2 F 2 ILE B 228 HIS B 229 1 O ILE B 228 N TYR B 192 SHEET 1 G 2 LYS B 216 TYR B 218 0 SHEET 2 G 2 ASP B 279 VAL B 281 1 O ASP B 279 N LEU B 217 SHEET 1 H 2 VAL B 224 ASP B 226 0 SHEET 2 H 2 GLU B 257 ASN B 259 -1 O LYS B 258 N ARG B 225 SITE 1 AC1 8 GLY A 53 ASP A 54 ARG A 55 HOH A6069 SITE 2 AC1 8 HOH A6132 HOH A6200 HOH A6203 HOH A6406 SITE 1 AC2 8 LYS A 258 THR A 309 ASP A 310 PHE A 311 SITE 2 AC2 8 SER A 312 HOH A6163 HOH A6188 HOH A6202 SITE 1 AC3 7 LYS B 258 THR B 309 ASP B 310 PHE B 311 SITE 2 AC3 7 SER B 312 HOH B6143 HOH B6263 SITE 1 AC4 36 ALA A 13 GLY A 14 PHE A 15 ILE A 16 SITE 2 AC4 36 ASP A 37 LYS A 38 LEU A 39 THR A 40 SITE 3 AC4 36 ALA A 42 GLY A 43 GLY A 61 ASP A 62 SITE 4 AC4 36 ILE A 63 TYR A 82 ALA A 83 ALA A 84 SITE 5 AC4 36 SER A 86 THR A 101 VAL A 123 SER A 124 SITE 6 AC4 36 TYR A 161 LYS A 165 CYS A 188 SER A 189 SITE 7 AC4 36 ASN A 190 ASN A 191 TDX A3500 HOH A6003 SITE 8 AC4 36 HOH A6005 HOH A6006 HOH A6007 HOH A6017 SITE 9 AC4 36 HOH A6026 HOH A6033 HOH A6038 HOH A6039 SITE 1 AC5 35 ALA B 13 GLY B 14 PHE B 15 ILE B 16 SITE 2 AC5 35 ASP B 37 LYS B 38 LEU B 39 THR B 40 SITE 3 AC5 35 ALA B 42 GLY B 43 GLY B 61 ASP B 62 SITE 4 AC5 35 ILE B 63 TYR B 82 ALA B 83 ALA B 84 SITE 5 AC5 35 SER B 86 THR B 101 VAL B 123 SER B 124 SITE 6 AC5 35 TYR B 161 LYS B 165 CYS B 188 ASN B 190 SITE 7 AC5 35 ASN B 191 TDX B4500 HOH B6005 HOH B6014 SITE 8 AC5 35 HOH B6017 HOH B6019 HOH B6021 HOH B6025 SITE 9 AC5 35 HOH B6027 HOH B6028 HOH B6046 SITE 1 AC6 13 SER A 86 ASN A 88 THR A 125 GLU A 127 SITE 2 AC6 13 TYR A 161 ASN A 190 LYS A 200 ARG A 225 SITE 3 AC6 13 ARG A 284 NAD A1400 HOH A6011 HOH A6028 SITE 4 AC6 13 HOH A6121 SITE 1 AC7 24 SER B 86 HIS B 87 ASN B 88 THR B 125 SITE 2 AC7 24 GLU B 127 TYR B 161 ASN B 190 GLU B 199 SITE 3 AC7 24 LYS B 200 PHE B 201 ARG B 204 GLN B 205 SITE 4 AC7 24 LYS B 216 TYR B 218 ARG B 225 ASN B 260 SITE 5 AC7 24 ARG B 284 HIS B 287 TYR B 340 NAD B2400 SITE 6 AC7 24 HOH B6023 HOH B6036 HOH B6040 HOH B6131 CRYST1 62.449 97.182 185.471 90.00 90.00 90.00 P 21 21 21 8 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 0.016013 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010290 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005392 0.00000