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

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Basic information

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


Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives / monosaccharide metabolic process / UDP-glucose 4-epimerase activity / galactose metabolic process / nucleotide 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-5'-DIPHOSPHATE-GLUCOSE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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)80,75910
Polymers77,9312
Non-polymers2,8288
Water13,872770
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-41 kcal/mol
Surface area25930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.933, 84.657, 73.514
Angle α, β, γ (deg.)90.000, 109.320, 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-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-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
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: Jul 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.25→27.224 Å / Num. obs: 191996 / % possible obs: 98.93 % / Redundancy: 6.6 % / CC1/2: 0.999 / Net I/σ(I): 15.81
Reflection shellResolution: 1.25→1.295 Å / Num. unique obs: 18989 / CC1/2: 0.664

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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: 1HZJ

1hzj


Resolution: 1.25→27.224 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1726 9711 5.06 %
Rwork0.145 182233 -
obs0.1464 191944 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.82 Å2 / Biso mean: 18.9068 Å2 / Biso min: 9.2 Å2
Refinement stepCycle: final / Resolution: 1.25→27.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5247 0 176 770 6193
Biso mean--20.02 30.08 -
Num. residues----680
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.25-1.26420.31573210.2623604998
1.2642-1.27910.29343010.2569592198
1.2791-1.29470.27973110.253607898
1.2947-1.31110.26162870.2423600598
1.3111-1.32830.29293210.2327602398
1.3283-1.34650.26113270.2294597798
1.3465-1.36570.25172810.2193593497
1.3657-1.38610.24973270.1977609699
1.3861-1.40780.24683160.1886604099
1.4078-1.43090.22923250.1771602299
1.4309-1.45550.21623630.1681603899
1.4555-1.4820.20193450.156604899
1.482-1.51050.18423330.1469608499
1.5105-1.54130.18083150.1422606799
1.5413-1.57490.18423250.1374598698
1.5749-1.61150.16733380.1244602099
1.6115-1.65180.15933310.11816121100
1.6518-1.69640.17593220.11716122100
1.6964-1.74630.15562930.12116145100
1.7463-1.80270.17273220.12466136100
1.8027-1.86710.17183440.12326113100
1.8671-1.94180.16323180.12976080100
1.9418-2.03020.15883040.1284611999
2.0302-2.13720.16423200.12536119100
2.1372-2.2710.15433170.12576184100
2.271-2.44630.15673400.13336160100
2.4463-2.69230.16323720.1446065100
2.6923-3.08140.1763290.1476608198
3.0814-3.88040.14823380.146182100
3.8804-27.2240.1473250.1419621899

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