HEADER OXIDOREDUCTASE 17-AUG-98 1GFS TITLE GDP-FUCOSE SYNTHETASE FROM E. COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: GDP-FUCOSE SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: WCAG, GDP-4-KETO 6-DEOXY-MANNOSE 3,5-EPIMERASE 4-REDUCTASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 CELLULAR_LOCATION: CYTOPLASM; SOURCE 6 GENE: WCAG; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 10 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PSEWCAG; SOURCE 12 EXPRESSION_SYSTEM_GENE: WCAG KEYWDS EPIMERASE-REDUCTASE, NADP, GDP-FUCOSE, LIPOPOLYSACCHARIDE KEYWDS 2 BIOSYNTHESIS, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR W.S.SOMERS,M.L.STAHL,F.X.SULLIVAN REVDAT 5 07-FEB-24 1GFS 1 REMARK REVDAT 4 13-JUL-11 1GFS 1 VERSN REVDAT 3 24-FEB-09 1GFS 1 VERSN REVDAT 2 12-MAY-00 1GFS 1 HEADER DBREF REVDAT 1 17-AUG-99 1GFS 0 JRNL AUTH W.S.SOMERS,M.L.STAHL,F.X.SULLIVAN JRNL TITL GDP-FUCOSE SYNTHETASE FROM ESCHERICHIA COLI: STRUCTURE OF A JRNL TITL 2 UNIQUE MEMBER OF THE SHORT-CHAIN DEHYDROGENASE/REDUCTASE JRNL TITL 3 FAMILY THAT CATALYZES TWO DISTINCT REACTIONS AT THE SAME JRNL TITL 4 ACTIVE SITE. JRNL REF STRUCTURE V. 6 1601 1998 JRNL REFN ISSN 0969-2126 JRNL PMID 9862812 JRNL DOI 10.1016/S0969-2126(98)00157-9 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 22894 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 SET) : 0.171 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2489 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 80 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.360 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1GFS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000173562. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : FEB-97 REMARK 200 TEMPERATURE (KELVIN) : 291.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23163 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 14.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.1000 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) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.8 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 FOR SHELL : 4.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: SHARP, X-PLOR 3.843 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.00 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 49.93333 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 24.96667 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 24.96667 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 49.93333 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 ARG A 320 REMARK 465 GLY A 321 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 36 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 37 CG OD1 OD2 REMARK 470 ARG A 45 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 55 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 174 CG ND1 CD2 CE1 NE2 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 GLN A 25 41.66 -85.49 REMARK 500 ARG A 26 130.65 -171.21 REMARK 500 LEU A 114 40.50 -103.28 REMARK 500 LEU A 240 64.90 -154.18 REMARK 500 ARG A 318 -16.58 -158.08 REMARK 500 REMARK 500 REMARK: NULL DBREF 1GFS A 1 321 UNP P32055 FCL_ECOLI 1 321 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 TYR 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 ASN 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 FORMUL 2 HOH *80(H2 O) HELIX 1 1 MET A 14 LEU A 23 1 10 HELIX 2 2 SER A 44 SER A 53 1 10 HELIX 3 3 ILE A 69 THR A 74 1 6 HELIX 4 4 PRO A 76 ASN A 97 1 22 HELIX 5 5 SER A 108 ILE A 110 5 3 HELIX 6 6 GLU A 121 GLU A 123 5 3 HELIX 7 7 PRO A 131 TYR A 154 5 24 HELIX 8 8 VAL A 180 ALA A 193 1 14 HELIX 9 9 VAL A 214 GLU A 226 1 13 HELIX 10 10 HIS A 229 ASN A 235 1 7 HELIX 11 11 ILE A 253 VAL A 264 1 12 HELIX 12 12 THR A 288 GLN A 292 1 5 HELIX 13 13 LEU A 301 ASN A 315 1 15 SHEET 1 A 6 VAL A 29 VAL A 32 0 SHEET 2 A 6 GLN A 4 ALA A 9 1 N GLN A 4 O GLU A 30 SHEET 3 A 6 GLN A 58 LEU A 61 1 N GLN A 58 O PHE A 7 SHEET 4 A 6 LYS A 101 LEU A 105 1 N LYS A 101 O VAL A 59 SHEET 5 A 6 ASP A 157 PRO A 163 1 N ASP A 157 O LEU A 102 SHEET 6 A 6 ILE A 243 VAL A 245 1 N ILE A 243 O 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 N LEU A 212 O ASN A 165 SHEET 1 C 2 ASP A 198 TRP A 202 0 SHEET 2 C 2 ARG A 269 ASP A 273 1 N ARG A 269 O VAL A 199 CISPEP 1 GLN A 117 PRO A 118 0 -0.01 CRYST1 104.200 104.200 74.900 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 0.009597 0.005541 0.000000 0.00000 SCALE2 0.000000 0.011082 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013351 0.00000