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- PDB-1bws: CRYSTAL STRUCTURE OF GDP-4-KETO-6-DEOXY-D-MANNOSE EPIMERASE/REDUC... -

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Basic information

Entry
Database: PDB / ID: 1bws
TitleCRYSTAL STRUCTURE OF GDP-4-KETO-6-DEOXY-D-MANNOSE EPIMERASE/REDUCTASE FROM ESCHERICHIA COLI A KEY ENZYME IN THE BIOSYNTHESIS OF GDP-L-FUCOSE
ComponentsPROTEIN (GDP-4-KETO-6-DEOXY-D-MANNOSE EPIMERASE/REDUCTASE)
KeywordsOXIDOREDUCTASE / EPIMERASE/REDUCTASE / GDP-L-FUCOSE BIOSYNTHESIS
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 / MIR / Resolution: 2.2 Å
AuthorsRizzi, M. / Tonetti, M. / Flora, A.D. / Bolognesi, M.
CitationJournal: Structure / Year: 1998
Title: GDP-4-keto-6-deoxy-D-mannose epimerase/reductase from Escherichia coli, a key enzyme in the biosynthesis of GDP-L-fucose, displays the structural characteristics of the RED protein homology superfamily.
Authors: Rizzi, M. / Tonetti, M. / Vigevani, P. / Sturla, L. / Bisso, A. / Flora, A.D. / Bordo, D. / Bolognesi, M.
History
DepositionSep 25, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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-4-KETO-6-DEOXY-D-MANNOSE EPIMERASE/REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9182
Polymers36,1731
Non-polymers7451
Water1,964109
1
A: PROTEIN (GDP-4-KETO-6-DEOXY-D-MANNOSE EPIMERASE/REDUCTASE)
hetero molecules

A: PROTEIN (GDP-4-KETO-6-DEOXY-D-MANNOSE EPIMERASE/REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8374
Polymers72,3462
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-y+1,x-y,z-1/31
2
A: PROTEIN (GDP-4-KETO-6-DEOXY-D-MANNOSE EPIMERASE/REDUCTASE)
hetero molecules

A: PROTEIN (GDP-4-KETO-6-DEOXY-D-MANNOSE EPIMERASE/REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8374
Polymers72,3462
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area5290 Å2
ΔGint-28 kcal/mol
Surface area25610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.200, 104.200, 75.880
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-4-KETO-6-DEOXY-D-MANNOSE EPIMERASE/REDUCTASE)


Mass: 36173.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / 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.: 109 / 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: 3.29 Å3/Da / Density % sol: 62.57 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Density % sol: 64 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.5 Mlithium sulphate1reservoir
20.1 MMES1reservoir
316 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 24481 / % possible obs: 99.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 13.6
Reflection
*PLUS
Num. measured all: 105130

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Processing

Software
NameVersionClassification
TNTrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.2→15 Å / σ(F): 0 /
Num. reflection% reflection
obs24481 99.7 %
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 48 109 2636
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg1.65
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / σ(F): 0 / Rfactor obs: 0.202 / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 1.65

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