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- PDB-1db3: E.COLI GDP-MANNOSE 4,6-DEHYDRATASE -

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Basic information

Entry
Database: PDB / ID: 1db3
TitleE.COLI GDP-MANNOSE 4,6-DEHYDRATASE
ComponentsGDP-MANNOSE 4,6-DEHYDRATASE
KeywordsLYASE / DEHYDRATASE / NADP / GDP-MANNOSE / GDP-FUCOSE
Function / homology
Function and homology information


GDP-mannose 4,6-dehydratase / GDP-mannose 4,6-dehydratase activity / colanic acid biosynthetic process / 'de novo' GDP-L-fucose biosynthetic process / NADP+ binding / protein homodimerization activity
Similarity search - Function
GDP-mannose 4,6-dehydratase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / 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
GDP-mannose 4,6-dehydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsSomoza, J.R. / Menon, S. / Somers, W.S. / Sullivan, F.X.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Structural and kinetic analysis of Escherichia coli GDP-mannose 4,6 dehydratase provides insights into the enzyme's catalytic mechanism and regulation by GDP-fucose.
Authors: Somoza, J.R. / Menon, S. / Schmidt, H. / Joseph-McCarthy, D. / Dessen, A. / Stahl, M.L. / Somers, W.S. / Sullivan, F.X.
History
DepositionNov 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GDP-MANNOSE 4,6-DEHYDRATASE


Theoretical massNumber of molelcules
Total (without water)41,9681
Polymers41,9681
Non-polymers00
Water2,036113
1
A: GDP-MANNOSE 4,6-DEHYDRATASE

A: GDP-MANNOSE 4,6-DEHYDRATASE


Theoretical massNumber of molelcules
Total (without water)83,9352
Polymers83,9352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)149.60, 149.60, 102.60
Angle α, β, γ (deg.)90, 90, 120
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein GDP-MANNOSE 4,6-DEHYDRATASE


Mass: 41967.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PT7GMD / Production host: Escherichia coli (E. coli) / References: UniProt: P0AC88, GDP-mannose 4,6-dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 3.95 Å3/Da / Density % sol: 68.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: SODIUM TARTRATE, HEPES, DTT, SODIUM CHLORIDE, TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
20.8 MNa/K tartrate1drop
350 mM1dropNaCl
450 mMHEPES1drop
510 mMTris-HCl1drop
61 mMdithiothreitol1drop
70.8 MNa/K tartrate1reservoir
8100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.2
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 30549 / Num. obs: 375043 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 29.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.526 / % possible all: 99.1
Reflection
*PLUS
Num. obs: 30549 / Num. measured all: 375043
Reflection shell
*PLUS
% possible obs: 99.1 % / Mean I/σ(I) obs: 5.35

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
ADSCdata collection
SCALEPACKdata scaling
RefinementResolution: 2.3→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3055 -RANDOM
Rwork0.205 ---
all0.205 30449 --
obs0.205 30449 99.8 %-
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2641 0 0 113 2754
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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