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Basic information

Entry
Database: PDB / ID: 7anh
TitleDdhaC
ComponentsGDP-L-fucose synthase
KeywordsSUGAR BINDING PROTEIN / reducatase / sugar nucleotide / sdr fold / enzyme
Function / homology
Function and homology information


GDP-L-fucose synthase / GDP-L-fucose synthase activity / 'de novo' GDP-L-fucose biosynthetic process / NADP+ binding / isomerase activity
Similarity search - Function
GDP-L-fucose synthase/GDP-L-colitose synthase / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
GDP-L-fucose synthase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsNaismith, J.H. / Woodward, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust100209/Z/12/Z) United Kingdom
CitationJournal: To Be Published
Title: DdhaC
Authors: Naismith, J.H. / Woodward, L.
History
DepositionOct 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GDP-L-fucose synthase


Theoretical massNumber of molelcules
Total (without water)40,5221
Polymers40,5221
Non-polymers00
Water1,56787
1
A: GDP-L-fucose synthase

A: GDP-L-fucose synthase


Theoretical massNumber of molelcules
Total (without water)81,0432
Polymers81,0432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3350 Å2
ΔGint-24 kcal/mol
Surface area30510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.801, 131.801, 50.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-416-

HOH

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Components

#1: Protein GDP-L-fucose synthase / NAD-dependent epimerase/dehydratase family protein


Mass: 40521.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter)
Gene: AY595_07840, B9Q63_05455, BB943_08725, D0W34_08630, D5I02_08530, DK813_08295, DQX79_06120, DW530_02880, F1P94_08750, FQZ47_07910, FRQ83_08390, FW031_08555, GAX04_08405, GRS20_08805, GSH24_ ...Gene: AY595_07840, B9Q63_05455, BB943_08725, D0W34_08630, D5I02_08530, DK813_08295, DQX79_06120, DW530_02880, F1P94_08750, FQZ47_07910, FRQ83_08390, FW031_08555, GAX04_08405, GRS20_08805, GSH24_04185, GY415_001379, GZD82_001462
Production host: Escherichia coli (E. coli) / References: UniProt: A0A5T1PRU5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 54 % (w/v) PEG 400, 0.1 M HEPES pH 7.5, 0.08 M ammonium citrate

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.08→99 Å / Num. obs: 25782 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.9 / Rmerge(I) obs: 0.163 / Net I/σ(I): 11.5
Reflection shellResolution: 2.08→2.14 Å / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1861 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BSV

1bsv


Resolution: 2.08→93.2 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.546 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 1372 5.1 %RANDOM
Rwork0.1904 ---
obs0.1926 25782 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.53 Å2 / Biso mean: 26.362 Å2 / Biso min: 8.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.87 Å2
Refinement stepCycle: final / Resolution: 2.08→93.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 0 87 2897
Biso mean---26.49 -
Num. residues----347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192864
X-RAY DIFFRACTIONr_bond_other_d0.0020.022818
X-RAY DIFFRACTIONr_angle_refined_deg1.8871.963851
X-RAY DIFFRACTIONr_angle_other_deg1.02836494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1575344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.56325.522134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.85215553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.191157
X-RAY DIFFRACTIONr_chiral_restr0.1170.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023189
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02652
LS refinement shellResolution: 2.08→2.133 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.297 82 -
Rwork0.241 1861 -
obs--98.43 %

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