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- PDB-7k3p: The structure of the UDP-Glc/GlcNAc 4-epimerase from the human pa... -

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Basic information

Entry
Database: PDB / ID: 7k3p
TitleThe structure of the UDP-Glc/GlcNAc 4-epimerase from the human pathogen Campylobacter jejuni
ComponentsUDP-glucose 4-epimerase
KeywordsSUGAR BINDING PROTEIN / NAD+/NADH-binding enzyme
Function / homology
Function and homology information


UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose metabolic process / nucleotide binding
Similarity search - Function
UDP-glucose 4-epimerase / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsYun, H.G. / Clemons Jr., W.M.
CitationJournal: Biorxiv / Year: 2020
Title: The structure of the UDP-Glc/GlcNAc 4-epimerase from the human pathogen Authors: Yun, H.G. / Jang, K.S. / Tanaka, S. / Clemons, W.M.
History
DepositionSep 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-glucose 4-epimerase
B: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,81313
Polymers76,7232
Non-polymers2,09011
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-38 kcal/mol
Surface area25120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.700, 87.700, 261.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein UDP-glucose 4-epimerase


Mass: 38361.535 Da / Num. of mol.: 2 / Mutation: Q45A, K46A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter)
Strain: ATCC 700819 / NCTC 11168 / Gene: gne, Cj1131c / Production host: Escherichia coli (E. coli) / References: UniProt: Q0P9C3, UDP-glucose 4-epimerase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.27 Å3/Da / Density % sol: 62.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: sodium acetate trihydrate, sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2013
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→65.42 Å / Num. obs: 65906 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 18
Reflection shellResolution: 2.04→2.09 Å / Rmerge(I) obs: 0.677 / Num. unique obs: 4348

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C20

2c20


Resolution: 2.04→62.013 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2252 6669 10.12 %
Rwork0.1953 59237 -
obs0.1982 65906 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.99 Å2 / Biso mean: 34.96 Å2 / Biso min: 15.93 Å2
Refinement stepCycle: final / Resolution: 2.04→62.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5152 0 144 167 5463
Biso mean--33.46 33.06 -
Num. residues----658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085397
X-RAY DIFFRACTIONf_angle_d1.067289
X-RAY DIFFRACTIONf_chiral_restr0.073804
X-RAY DIFFRACTIONf_plane_restr0.004926
X-RAY DIFFRACTIONf_dihedral_angle_d14.361976
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.04-2.06320.29731990.25671932100
2.0632-2.08750.3071990.25621973100
2.0875-2.11290.26142500.24671886100
2.1129-2.13970.30692270.24151974100
2.1397-2.16780.25762270.23191899100
2.1678-2.19750.25292060.21931964100
2.1975-2.22890.2332140.21331945100
2.2289-2.26220.23292040.22261967100
2.2622-2.29750.27692350.22841938100
2.2975-2.33520.25672100.22241953100
2.3352-2.37550.26332090.22071959100
2.3755-2.41870.28442510.2261914100
2.4187-2.46520.25822190.2171948100
2.4652-2.51550.25082540.21111944100
2.5155-2.57020.26342140.21011945100
2.5702-2.630.25822110.21191970100
2.63-2.69580.25012330.21161951100
2.6958-2.76870.24692380.22261944100
2.7687-2.85010.30872100.22291990100
2.8501-2.94210.25172150.21961974100
2.9421-3.04730.25012130.21761982100
3.0473-3.16930.26072380.22271962100
3.1693-3.31350.23362170.21531991100
3.3135-3.48820.22641990.1979200799
3.4882-3.70670.22932210.1881995100
3.7067-3.99290.21791970.17532055100
3.9929-4.39460.19432370.16881993100
4.3946-5.03020.16992410.15112031100
5.0302-6.33660.20032310.1733206699
6.3366-62.0130.1682500.172218599

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