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- PDB-8ewu: X-ray structure of the GDP-6-deoxy-4-keto-D-lyxo-heptose-4-reduct... -

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Basic information

Entry
Database: PDB / ID: 8ewu
TitleX-ray structure of the GDP-6-deoxy-4-keto-D-lyxo-heptose-4-reductase from Campylobacter jejuni HS:15
ComponentsGDP-L-fucose synthase
KeywordsBIOSYNTHETIC PROTEIN / OXIDOREDUCTASE / capsular polysaccharide / reductase
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
GUANOSINE-5'-DIPHOSPHATE / Chem-NDP / GDP-L-fucose synthase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsThoden, J.B. / Xiang, D.F. / Ghosh, M.K. / Riegert, A.S. / Raushel, F.M. / Holden, H.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM139428 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122825 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM134643 United States
CitationJournal: Biochemistry / Year: 2023
Title: Bifunctional Epimerase/Reductase Enzymes Facilitate the Modulation of 6-Deoxy-Heptoses Found in the Capsular Polysaccharides of Campylobacter jejuni.
Authors: Xiang, D.F. / Ghosh, M.K. / Riegert, A.S. / Thoden, J.B. / Holden, H.M. / Raushel, F.M.
History
DepositionOct 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)88,8448
Polymers86,3432
Non-polymers2,5016
Water12,556697
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-36 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.761, 56.625, 67.380
Angle α, β, γ (deg.)87.960, 81.960, 70.120
Int Tables number1
Space group name H-MP1

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Components

#1: Protein GDP-L-fucose synthase /


Mass: 43171.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: HS:15 / Gene: fcl, HS15.12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2(DE3) / References: UniProt: F2X7A6, GDP-L-fucose synthase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 697 / 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: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein pre-incubated with 5.0 mM GDP, 5.0 mM NADPH. Precipitant: 18-22% PEG3350, 2% isopropanol, 100 mM HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 121498 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rsym value: 0.049 / Net I/σ(I): 18.4
Reflection shellResolution: 1.45→1.55 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 20129 / Rsym value: 0.338 / % possible all: 87.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7M13

7m13


Resolution: 1.45→33.38 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.782 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 6098 5 %RANDOM
Rwork0.1884 ---
obs0.1899 115400 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.24 Å2 / Biso mean: 16.068 Å2 / Biso min: 5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.45→33.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5739 0 160 700 6599
Biso mean--12.3 25.99 -
Num. residues----707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136150
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175683
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.6618336
X-RAY DIFFRACTIONr_angle_other_deg1.4911.58613286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6755748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.27624.474304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.435151156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.3491518
X-RAY DIFFRACTIONr_chiral_restr0.090.2811
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026734
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021230
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 392 -
Rwork0.415 7734 -
all-8126 -
obs--86.12 %

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