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- PDB-7anc: MlghC, GDP-mannoheptose C4 reductase from Campylobacter jejuni wi... -

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Basic information

Entry
Database: PDB / ID: 7anc
TitleMlghC, GDP-mannoheptose C4 reductase from Campylobacter jejuni with NADP bound
ComponentsGDP-L-fucose synthase
KeywordsSUGAR BINDING PROTEIN / reductase / sugar nucleotide / NADP / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / GDP-L-fucose synthase / GDP-L-fucose synthase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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: MghlC
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

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Assembly

Deposited unit
A: GDP-L-fucose synthase
B: GDP-L-fucose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0814
Polymers78,5942
Non-polymers1,4872
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-25 kcal/mol
Surface area27650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.800, 131.960, 59.330
Angle α, β, γ (deg.)90.00, 105.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GDP-L-fucose synthase / GDP-4-keto-6-deoxy-D-mannose-3 / 5-epimerase-4-reductase


Mass: 39297.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter)
Gene: fcl, A0Z41_07385, A4277_09460, B4O43_09695, B7M65_03500, BGG25_09085, BM409_09645, BM444_09020, BM513_08725, BSK70_08245, BSO22_09170, C1418_09205, CLC11_09615, CUT57_09340, D6H09_04540, DDV78_ ...Gene: fcl, A0Z41_07385, A4277_09460, B4O43_09695, B7M65_03500, BGG25_09085, BM409_09645, BM444_09020, BM513_08725, BSK70_08245, BSO22_09170, C1418_09205, CLC11_09615, CUT57_09340, D6H09_04540, DDV78_09315, DMN69_08810, DNA92_09025, DYU98_09465, E7P31_08700, E7R39_08755, EID41_09375, F0F26_01770, F0G48_09060, F0N28_08130, F0N82_00455, F1N65_08775, F1O83_08585, F6069_09545, F7N67_09870, F9736_08790, FJ686_08865, FLI41_08640, FM724_09175, FNW64_09505, FVI37_08605, FVM38_08200, FVN10_08680, FVY82_08620, FWZ78_00530, FXA21_08565, FXA45_08500, FY829_09130, FYZ21_00200, FZ860_03225, FZB49_04250, FZJ28_08760, FZL73_00555, GAU91_08635, GAX51_09535, GCY42_03575, GI310_08960, GLM81_05635, GLM94_08710, GPY87_09235, GS576_08295, GTQ72_08225, GV351_09045, GWW43_07690, GXS63_001732, GZD67_001693
Production host: Escherichia coli (E. coli)
References: UniProt: A0A2U0QM62, UniProt: Q0P8I6*PLUS, GDP-L-fucose synthase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.75 Å3/Da / Density % sol: 55.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 24.63 % (w/v) PEG 8000, 0.1 M Bicine pH 8.5, 0.12 M sodium citrate 0.05 % (w/v).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.66→66 Å / Num. obs: 94907 / % possible obs: 99.2 % / Redundancy: 3.7 % / CC1/2: 1 / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.8
Reflection shellResolution: 1.66→1.7 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.76 / Num. unique obs: 7016 / CC1/2: 0.5 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BSV

1bsv


Resolution: 1.66→65.98 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.229 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20231 4889 4.9 %RANDOM
Rwork0.17273 ---
obs0.17416 94907 99.17 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.453 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0.01 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.66→65.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5187 0 96 414 5697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195394
X-RAY DIFFRACTIONr_bond_other_d0.0010.024995
X-RAY DIFFRACTIONr_angle_refined_deg1.491.8877277
X-RAY DIFFRACTIONr_angle_other_deg1.2052.92511608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8035644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98525.121248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7515973
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8981516
X-RAY DIFFRACTIONr_chiral_restr0.1030.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025896
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021082
X-RAY DIFFRACTIONr_mcbond_it3.3592.3132594
X-RAY DIFFRACTIONr_mcbond_other3.3592.3112593
X-RAY DIFFRACTIONr_mcangle_it4.4383.4363229
X-RAY DIFFRACTIONr_mcangle_other4.4373.4383230
X-RAY DIFFRACTIONr_scbond_it5.1672.832800
X-RAY DIFFRACTIONr_scbond_other5.1692.8292798
X-RAY DIFFRACTIONr_scangle_other7.3864.0314048
X-RAY DIFFRACTIONr_long_range_B_refined8.5827.7065781
X-RAY DIFFRACTIONr_long_range_B_other8.55427.3615705
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 380 -
Rwork0.324 7016 -
obs--99.08 %

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