PDB Short entry for 1E7R HEADER ISOMERASE 07-SEP-00 1E7R TITLE GDP 4-KETO-6-DEOXY-D-MANNOSE EPIMERASE REDUCTASE Y136E COMPND MOL_ID: 1; COMPND 2 MOLECULE: GDP-FUCOSE SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GDP-4-KETO 6-DEOXY-MANNOSE 3,5-EPIMERASE 4-REDUCTASE, GMER; COMPND 5 EC: 5.1.3.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: UNKNOWN MOLECULE LABELED AS ACETYLPHOSPHATE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS EPIMERASE, REDUCTASE, SDR, RED, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.ROSANO,G.IZZO,M.BOLOGNESI REVDAT 6 13-DEC-23 1E7R 1 REMARK REVDAT 5 24-JUL-19 1E7R 1 REMARK REVDAT 4 08-MAY-19 1E7R 1 REMARK REVDAT 3 01-SEP-09 1E7R 1 HEADER KEYWDS REMARK DBREF REVDAT 2 24-FEB-09 1E7R 1 VERSN REVDAT 1 18-OCT-00 1E7R 0 JRNL AUTH C.ROSANO,A.BISSO,G.IZZO,M.TONETTI,L.STURLA,A.DE FLORA, JRNL AUTH 2 M.BOLOGNESI JRNL TITL PROBING THE CATALYTIC MECHANISM OF JRNL TITL 2 GDP-4-KETO-6-DEOXY-D-MANNOSE EPIMERASE/REDUCTASE BY KINETIC JRNL TITL 3 AND CRYSTALLOGRAPHIC CHARACTERIZATION OF SITE-SPECIFIC JRNL TITL 4 MUTANTS JRNL REF J.MOL.BIOL. V. 303 77 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 11021971 JRNL DOI 10.1006/JMBI.2000.4106 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 57354 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2480 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 82 REMARK 3 SOLVENT ATOMS : 347 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.069 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.071 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.017 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.038 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.031 ; 0.040 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1E7R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-SEP-00. REMARK 100 THE DEPOSITION ID IS D_1290005089. 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 : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.844 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61196 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.6500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 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: PDB ENTRY 1BWS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M LITHIUM SULPHATE, PH 6.5 0.1M REMARK 280 TRIS BUFFER 21C, PH 6.50, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 50.00000 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 25.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 50.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 25.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 CHAIN A ENGINEERED MUTATION TYR136GLU REMARK 400 NADP-DEPENDENT CONVERSION OF GDP-4-DEHYDRO-6-DEOXY-D-MANNOSE REMARK 400 TO GDP-FUCOSE. REMARK 400 INVOLVED IN THE BIOSYNTHESIS OF THE SLIME POLYSACCHARIDE REMARK 400 COLANIC ACID. 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 ASP A 317 REMARK 465 ARG A 318 REMARK 465 PHE A 319 REMARK 465 ARG A 320 REMARK 465 GLY A 321 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 25 CD OE1 NE2 REMARK 480 GLU A 30 CD OE1 OE2 REMARK 480 ASP A 37 CG OD1 OD2 REMARK 480 ARG A 45 CG CD NE CZ NH1 NH2 REMARK 480 ARG A 55 CD NE CZ NH1 NH2 REMARK 480 LYS A 113 CE NZ REMARK 480 LYS A 116 CD CE NZ REMARK 480 GLU A 230 CD OE1 OE2 REMARK 480 GLU A 234 CG CD OE1 OE2 REMARK 480 ARG A 269 NE CZ NH1 NH2 REMARK 480 LYS A 283 CE NZ 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 NH1 ARG A 269 O HOH A 2269 0.31 REMARK 500 CD2 TYR A 266 O HOH A 2262 0.78 REMARK 500 N GLN A 237 O HOH A 2239 0.78 REMARK 500 C VAL A 199 O HOH A 2213 0.83 REMARK 500 CZ ARG A 269 O HOH A 2269 1.11 REMARK 500 NE2 GLN A 153 O HOH A 2176 1.32 REMARK 500 CA VAL A 199 O HOH A 2213 1.32 REMARK 500 CD GLN A 153 O HOH A 2176 1.35 REMARK 500 C3 TRS A 1319 O HOH A 2338 1.49 REMARK 500 O2 TRS A 1319 O HOH A 2341 1.54 REMARK 500 CG TYR A 266 O HOH A 2262 1.57 REMARK 500 CA GLN A 237 O HOH A 2239 1.58 REMARK 500 N VAL A 200 O HOH A 2213 1.60 REMARK 500 O VAL A 199 O HOH A 2213 1.61 REMARK 500 O HOH A 2253 O HOH A 2254 1.63 REMARK 500 C THR A 236 O HOH A 2239 1.63 REMARK 500 CE2 TYR A 266 O HOH A 2262 1.66 REMARK 500 O HOH A 2219 O HOH A 2220 1.70 REMARK 500 O1 TRS A 1319 O HOH A 2338 1.77 REMARK 500 O HOH A 2186 O HOH A 2292 1.78 REMARK 500 C1 TRS A 1319 O HOH A 2338 1.84 REMARK 500 C TRS A 1319 O HOH A 2338 1.88 REMARK 500 CG GLN A 153 O HOH A 2176 1.91 REMARK 500 O HOH A 2307 O HOH A 2312 1.94 REMARK 500 NH2 ARG A 269 O HOH A 2269 1.99 REMARK 500 CB VAL A 199 O HOH A 2213 2.01 REMARK 500 O HOH A 2168 O HOH A 2169 2.04 REMARK 500 O HOH A 2060 O HOH A 2111 2.05 REMARK 500 O ASN A 72 O HOH A 2085 2.15 REMARK 500 O HOH A 2107 O HOH A 2289 2.15 REMARK 500 O3B NAP A 1317 O HOH A 2330 2.15 REMARK 500 O HOH A 2268 O HOH A 2270 2.17 REMARK 500 O3 TRS A 1322 O HOH A 2346 2.17 REMARK 500 OE1 GLU A 130 O HOH A 2160 2.17 REMARK 500 O HOH A 2054 O HOH A 2168 2.18 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 2110 O HOH A 2110 5555 0.92 REMARK 500 O HOH A 2111 O HOH A 2111 5555 1.84 REMARK 500 O HOH A 2164 O HOH A 2168 5555 2.13 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 ARG A 55 CG ARG A 55 CD 0.206 REMARK 500 LYS A 113 CD LYS A 113 CE -0.236 REMARK 500 LEU A 114 CG LEU A 114 CD1 0.263 REMARK 500 GLU A 230 CG GLU A 230 CD 1.977 REMARK 500 GLU A 234 CB GLU A 234 CG -0.125 REMARK 500 CYS A 251 CB CYS A 251 SG -0.096 REMARK 500 LYS A 283 CD LYS A 283 CE 0.248 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 ARG A 5 CD - NE - CZ ANGL. DEV. = 12.3 DEGREES REMARK 500 ARG A 20 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 21 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 26 CD - NE - CZ ANGL. DEV. = 21.8 DEGREES REMARK 500 ARG A 26 NH1 - CZ - NH2 ANGL. DEV. = 9.4 DEGREES REMARK 500 ARG A 26 NE - CZ - NH1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG A 26 NE - CZ - NH2 ANGL. DEV. = -16.2 DEGREES REMARK 500 ARG A 34 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 36 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ASP A 37 CB - CG - OD1 ANGL. DEV. = 7.4 DEGREES REMARK 500 ASP A 37 CB - CG - OD2 ANGL. DEV. = -7.2 DEGREES REMARK 500 ASP A 98 CB - CG - OD2 ANGL. DEV. = -8.9 DEGREES REMARK 500 LEU A 114 CB - CG - CD1 ANGL. DEV. = -25.5 DEGREES REMARK 500 LEU A 124 CB - CG - CD2 ANGL. DEV. = 24.4 DEGREES REMARK 500 GLU A 130 OE1 - CD - OE2 ANGL. DEV. = 8.2 DEGREES REMARK 500 ARG A 152 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 152 NE - CZ - NH2 ANGL. DEV. = -7.0 DEGREES REMARK 500 TYR A 167 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 TYR A 167 CB - CG - CD1 ANGL. DEV. = 4.0 DEGREES REMARK 500 SER A 195 N - CA - CB ANGL. DEV. = 9.9 DEGREES REMARK 500 ARG A 209 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 209 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 GLU A 230 CB - CG - CD ANGL. DEV. = -79.4 DEGREES REMARK 500 GLU A 230 CG - CD - OE1 ANGL. DEV. = -24.9 DEGREES REMARK 500 GLU A 230 CG - CD - OE2 ANGL. DEV. = 22.4 DEGREES REMARK 500 CYS A 251 N - CA - CB ANGL. DEV. = -12.5 DEGREES REMARK 500 TYR A 266 CB - CG - CD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP A 273 CB - CG - OD2 ANGL. DEV. = -8.3 DEGREES REMARK 500 ASP A 286 CB - CG - OD1 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 289 CG - CD - NE ANGL. DEV. = -13.8 DEGREES REMARK 500 ARG A 289 NH1 - CZ - NH2 ANGL. DEV. = 12.0 DEGREES REMARK 500 ARG A 289 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 289 NE - CZ - NH2 ANGL. DEV. = -7.6 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 THR A 164 -168.47 -79.28 REMARK 500 PHE A 173 46.62 -89.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ASP A 98 0.09 SIDE CHAIN REMARK 500 GLU A 123 0.08 SIDE CHAIN REMARK 500 GLN A 126 0.11 SIDE CHAIN REMARK 500 GLU A 255 0.07 SIDE CHAIN REMARK 500 TYR A 266 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLN A 25 -17.37 REMARK 500 SER A 176 -11.82 REMARK 500 VAL A 199 -12.76 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 A2030 DISTANCE = 7.75 ANGSTROMS REMARK 525 HOH A2036 DISTANCE = 5.85 ANGSTROMS 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 1320 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1321 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP A 1317 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UVW A 1318 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 1319 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 1322 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BSV RELATED DB: PDB REMARK 900 GDP-FUCOSE SYNTHETASE FROM ESCHERICHIA COLI COMPLEX WITH NADPH REMARK 900 RELATED ID: 1BWS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GDP-4-KETO-6-DEOXY-D-MANNOSE EPIMERASE/ REMARK 900 REDUCTASE FROM ESCHERICHIA COLI A KEY ENZYME IN THE BIOSYNTHESIS OF REMARK 900 GDP-L-FUCOSE REMARK 900 RELATED ID: 1E6U RELATED DB: PDB REMARK 900 GDP 4-KETO-6-DEOXY-D-MANNOSE EPIMERASE REDUCTASE REMARK 900 RELATED ID: 1E7Q RELATED DB: PDB REMARK 900 GDP 4-KETO-6-DEOXY-D-MANNOSE EPIMERASE REDUCTASE S107A REMARK 900 RELATED ID: 1E7S RELATED DB: PDB REMARK 900 GDP 4-KETO-6-DEOXY-D-MANNOSE EPIMERASE REDUCTASE K140R REMARK 900 RELATED ID: 1FXS RELATED DB: PDB REMARK 900 GDP-FUCOSE SYNTHETASE FROM ESCHERICHIA COLI COMPLEX WITH NADP REMARK 900 RELATED ID: 1GFS RELATED DB: PDB REMARK 900 GDP-FUCOSE SYNTHETASE FROM E. COLI DBREF 1E7R A 1 321 UNP P32055 FCL_ECOLI 1 321 SEQADV 1E7R GLU A 136 UNP P32055 TYR 136 ENGINEERED MUTATION SEQADV 1E7R SER A 195 UNP P32055 ASN 195 CONFLICT SEQRES 1 A 321 MET SER LYS GLN ARG VAL PHE ILE ALA GLY HIS ARG GLY SEQRES 2 A 321 MET VAL GLY SER ALA ILE ARG ARG GLN LEU GLU GLN ARG SEQRES 3 A 321 GLY ASP VAL GLU LEU VAL LEU ARG THR ARG ASP GLU LEU SEQRES 4 A 321 ASN LEU LEU ASP SER ARG ALA VAL HIS ASP PHE PHE ALA SEQRES 5 A 321 SER GLU ARG ILE ASP GLN VAL TYR LEU ALA ALA ALA LYS SEQRES 6 A 321 VAL GLY GLY ILE VAL ALA ASN ASN THR TYR PRO ALA ASP SEQRES 7 A 321 PHE ILE TYR GLN ASN MET MET ILE GLU SER ASN ILE ILE SEQRES 8 A 321 HIS ALA ALA HIS GLN ASN ASP VAL ASN LYS LEU LEU PHE SEQRES 9 A 321 LEU GLY SER SER CYS ILE TYR PRO LYS LEU ALA LYS GLN SEQRES 10 A 321 PRO MET ALA GLU SER GLU LEU LEU GLN GLY THR LEU GLU SEQRES 11 A 321 PRO THR ASN GLU PRO GLU ALA ILE ALA LYS ILE ALA GLY SEQRES 12 A 321 ILE LYS LEU CYS GLU SER TYR ASN ARG GLN TYR GLY ARG SEQRES 13 A 321 ASP TYR ARG SER VAL MET PRO THR ASN LEU TYR GLY PRO SEQRES 14 A 321 HIS ASP ASN PHE HIS PRO SER ASN SER HIS VAL ILE PRO SEQRES 15 A 321 ALA LEU LEU ARG ARG PHE HIS GLU ALA THR ALA GLN SER SEQRES 16 A 321 ALA PRO ASP VAL VAL VAL TRP GLY SER GLY THR PRO MET SEQRES 17 A 321 ARG GLU PHE LEU HIS VAL ASP ASP MET ALA ALA ALA SER SEQRES 18 A 321 ILE HIS VAL MET GLU LEU ALA HIS GLU VAL TRP LEU GLU SEQRES 19 A 321 ASN THR GLN PRO MET LEU SER HIS ILE ASN VAL GLY THR SEQRES 20 A 321 GLY VAL ASP CYS THR ILE ARG GLU LEU ALA GLN THR ILE SEQRES 21 A 321 ALA LYS VAL VAL GLY TYR LYS GLY ARG VAL VAL PHE ASP SEQRES 22 A 321 ALA SER LYS PRO ASP GLY THR PRO ARG LYS LEU LEU ASP SEQRES 23 A 321 VAL THR ARG LEU HIS GLN LEU GLY TRP TYR HIS GLU ILE SEQRES 24 A 321 SER LEU GLU ALA GLY LEU ALA SER THR TYR GLN TRP PHE SEQRES 25 A 321 LEU GLU ASN GLN ASP ARG PHE ARG GLY HET NAP A1317 48 HET UVW A1318 8 HET TRS A1319 8 HET SO4 A1320 5 HET SO4 A1321 5 HET TRS A1322 8 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM UVW ACETYLPHOSPHATE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM SO4 SULFATE ION HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE HETSYN TRS TRIS BUFFER FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 UVW C2 H5 O5 P FORMUL 4 TRS 2(C4 H12 N O3 1+) FORMUL 5 SO4 2(O4 S 2-) FORMUL 8 HOH *347(H2 O) HELIX 1 1 GLY A 13 GLU A 24 1 12 HELIX 2 2 ASP A 43 ARG A 55 1 13 HELIX 3 3 GLY A 68 TYR A 75 1 8 HELIX 4 4 TYR A 75 ASN A 97 1 23 HELIX 5 5 SER A 107 TYR A 111 5 5 HELIX 6 6 ALA A 120 LEU A 124 5 5 HELIX 7 7 GLU A 130 THR A 132 5 3 HELIX 8 8 ASN A 133 GLY A 155 1 23 HELIX 9 9 HIS A 179 SER A 195 1 17 HELIX 10 10 VAL A 214 LEU A 227 1 14 HELIX 11 11 ALA A 228 ASN A 235 1 8 HELIX 12 12 ILE A 253 GLY A 265 1 13 HELIX 13 13 VAL A 287 LEU A 293 1 7 HELIX 14 14 SER A 300 ASN A 315 1 16 SHEET 1 A 6 VAL A 29 VAL A 32 0 SHEET 2 A 6 GLN A 4 ALA A 9 1 O GLN A 4 N GLU A 30 SHEET 3 A 6 GLN A 58 LEU A 61 1 O GLN A 58 N PHE A 7 SHEET 4 A 6 LYS A 101 LEU A 105 1 O LYS A 101 N VAL A 59 SHEET 5 A 6 ASP A 157 PRO A 163 1 O ASP A 157 N LEU A 102 SHEET 6 A 6 ILE A 243 VAL A 245 1 O ILE A 243 N MET A 162 SHEET 1 B 2 ASN A 165 TYR A 167 0 SHEET 2 B 2 PHE A 211 HIS A 213 1 O LEU A 212 N TYR A 167 SHEET 1 C 2 ASP A 198 TRP A 202 0 SHEET 2 C 2 ARG A 269 ASP A 273 1 O ARG A 269 N VAL A 199 SHEET 1 D 2 MET A 208 ARG A 209 0 SHEET 2 D 2 CYS A 251 THR A 252 -1 O CYS A 251 N ARG A 209 CISPEP 1 GLN A 117 PRO A 118 0 -9.25 SITE 1 AC1 4 HIS A 11 ARG A 12 ARG A 20 THR A 35 SITE 1 AC2 9 ARG A 152 PRO A 238 ARG A 254 VAL A 270 SITE 2 AC2 9 VAL A 271 PHE A 272 HOH A2343 HOH A2344 SITE 3 AC2 9 HOH A2345 SITE 1 AC3 33 GLY A 10 GLY A 13 MET A 14 VAL A 15 SITE 2 AC3 33 ARG A 36 LEU A 39 ASN A 40 LEU A 41 SITE 3 AC3 33 LEU A 42 ALA A 62 ALA A 63 ALA A 64 SITE 4 AC3 33 VAL A 66 ILE A 86 LEU A 105 GLY A 106 SITE 5 AC3 33 SER A 107 LYS A 140 PRO A 163 THR A 164 SITE 6 AC3 33 LEU A 166 HOH A2101 HOH A2323 HOH A2324 SITE 7 AC3 33 HOH A2325 HOH A2326 HOH A2327 HOH A2328 SITE 8 AC3 33 HOH A2329 HOH A2330 HOH A2331 HOH A2332 SITE 9 AC3 33 HOH A2333 SITE 1 AC4 9 GLY A 67 GLY A 68 ILE A 69 VAL A 70 SITE 2 AC4 9 ALA A 71 SER A 178 LYS A 262 HOH A2335 SITE 3 AC4 9 HOH A2336 SITE 1 AC5 13 ASP A 78 TYR A 81 GLN A 82 HIS A 92 SITE 2 AC5 13 HIS A 95 TYR A 150 GLN A 153 TYR A 154 SITE 3 AC5 13 HOH A2337 HOH A2338 HOH A2339 HOH A2341 SITE 4 AC5 13 HOH A2342 SITE 1 AC6 6 ARG A 20 ARG A 21 HIS A 170 TRP A 311 SITE 2 AC6 6 HOH A2346 HOH A2347 CRYST1 103.300 103.300 75.000 90.00 90.00 120.00 P 32 2 1 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 0.009680 0.005589 0.000000 0.00000 SCALE2 0.000000 0.011178 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013333 0.00000