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- PDB-7xpq: Crystal Structure of UDP-Glc/GlcNAc 4-Epimerase with NAD/UDP-GlcNAc -

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Basic information

Entry
Database: PDB / ID: 7xpq
TitleCrystal Structure of UDP-Glc/GlcNAc 4-Epimerase with NAD/UDP-GlcNAc
ComponentsUDP-glucose 4-epimerase
KeywordsPLANT PROTEIN / Epimerase / Complex / NAD / UDP-GlcNAc
Function / homology
Function and homology information


Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives / UDP-glucose 4-epimerase activity / galactose metabolic process / rRNA processing / nucleotide binding / RNA binding / cytosol
Similarity search - Function
UDP-glucose 4-epimerase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsChen, Y.H. / Wang, X.C. / Zhang, C.R.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Nat Commun / Year: 2023
Title: A maize epimerase modulates cell wall synthesis and glycosylation during stomatal morphogenesis.
Authors: Zhou, Y. / Zhang, T. / Wang, X. / Wu, W. / Xing, J. / Li, Z. / Qiao, X. / Zhang, C. / Wang, X. / Wang, G. / Li, W. / Bai, S. / Li, Z. / Suo, Y. / Wang, J. / Niu, Y. / Zhang, J. / Lan, C. / ...Authors: Zhou, Y. / Zhang, T. / Wang, X. / Wu, W. / Xing, J. / Li, Z. / Qiao, X. / Zhang, C. / Wang, X. / Wang, G. / Li, W. / Bai, S. / Li, Z. / Suo, Y. / Wang, J. / Niu, Y. / Zhang, J. / Lan, C. / Hu, Z. / Li, B. / Zhang, X. / Wang, W. / Galbraith, D.W. / Chen, Y. / Guo, S. / Song, C.P.
History
DepositionMay 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 6, 2023Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)80,4726
Polymers77,9312
Non-polymers2,5424
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-36 kcal/mol
Surface area25740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.873, 84.945, 73.436
Angle α, β, γ (deg.)90.000, 110.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UDP-glucose 4-epimerase / UDP-Glc/GlcNAc Epimerase


Mass: 38965.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 542127, ZEAMMB73_Zm00001d029151 / Production host: Escherichia coli (E. coli)
References: UniProt: C0HI30, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives
#2: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: 0.1M Sodium malonate pH 5.0, 12% w/V PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.15→20.077 Å / Num. obs: 40224 / % possible obs: 96.68 % / Redundancy: 7 % / CC1/2: 0.991 / Net I/σ(I): 6.42
Reflection shellResolution: 2.15→2.227 Å / Num. unique obs: 3959 / CC1/2: 0.197

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XPO

7xpo


Resolution: 2.15→20.077 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 1972 4.91 %
Rwork0.1972 38176 -
obs0.1998 40148 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.99 Å2 / Biso mean: 35.4897 Å2 / Biso min: 17.15 Å2
Refinement stepCycle: final / Resolution: 2.15→20.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5198 0 158 405 5761
Biso mean--36.78 40.5 -
Num. residues----678
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.15-2.20370.3981630.3613263796
2.2037-2.26320.39741490.3304264196
2.2632-2.32970.33591370.3164269196
2.3297-2.40480.34041230.2898270597
2.4048-2.49060.3171460.2666271297
2.4906-2.59010.30931450.2464270897
2.5901-2.70770.311240.2422274698
2.7077-2.85010.28841300.2328275398
2.8501-3.02810.29451240.2035275298
3.0281-3.2610.2481500.1945273698
3.261-3.58750.22821710.1771271898
3.5875-4.10280.20841330.1495278498
4.1028-5.15460.18121380.1369277998
5.1546-20.0770.19121390.1569281498

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