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- PDB-1bsv: GDP-FUCOSE SYNTHETASE FROM ESCHERICHIA COLI COMPLEX WITH NADPH -

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Basic information

Entry
Database: PDB / ID: 1bsv
TitleGDP-FUCOSE SYNTHETASE FROM ESCHERICHIA COLI COMPLEX WITH NADPH
ComponentsPROTEIN (GDP-FUCOSE SYNTHETASE)
KeywordsOXIDOREDUCTASE / EPIMERASE-REDUCTASE / NADPH / GDP-FUCOSE
Function / homology
Function and homology information


GDP-L-fucose synthase / GDP-L-fucose synthase activity / colanic acid biosynthetic process / 'de novo' GDP-L-fucose biosynthetic process / NADP+ binding / isomerase activity / protein homodimerization activity / cytoplasm
Similarity search - Function
GDP-L-fucose synthase/GDP-L-colitose synthase / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / GDP-L-fucose synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSomers, W.S. / Stahl, M.L. / Sullivan, F.X.
CitationJournal: Structure / Year: 1998
Title: GDP-fucose synthetase from Escherichia coli: structure of a unique member of the short-chain dehydrogenase/reductase family that catalyzes two distinct reactions at the same active site.
Authors: Somers, W.S. / Stahl, M.L. / Sullivan, F.X.
History
DepositionAug 31, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 26, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (GDP-FUCOSE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9332
Polymers36,1871
Non-polymers7451
Water1,51384
1
A: PROTEIN (GDP-FUCOSE SYNTHETASE)
hetero molecules

A: PROTEIN (GDP-FUCOSE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8654
Polymers72,3742
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5490 Å2
ΔGint-30 kcal/mol
Surface area25220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.300, 104.300, 74.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PROTEIN (GDP-FUCOSE SYNTHETASE) / WCAG / GDP-4-KETO 6-DEOXY-MANNOSE 3 / 5-EPIMERASE 4-REDUCTASE


Mass: 36187.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Cellular location: CYTOPLASM / Gene: WCAG / Plasmid: PSEWCAG / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): WCAG / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: P32055
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.14 %
Crystal growpH: 7 / Details: 4.0 M SODIUM FORMATE, pH 7
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
210 mMTris-HCl1drop
350 mMsodium chloride1drop
44.0 Msodium formate1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 15, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→14 Å / Num. obs: 24049 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 26.4
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 4.4 / % possible all: 96.7
Reflection shell
*PLUS
% possible obs: 96.7 %

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Processing

Software
NameVersionClassification
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GFS

1gfs


Resolution: 2.2→14 Å / σ(F): 2 /
RfactorNum. reflection% reflection
obs0.17 23752 98.4 %
Refinement stepCycle: LAST / Resolution: 2.2→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 48 84 2630
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.38
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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