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- PDB-5xvs: Crystal structure of UDP-GlcNAc 2-epimerase NeuC complexed with UDP -

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Basic information

Entry
Database: PDB / ID: 5xvs
TitleCrystal structure of UDP-GlcNAc 2-epimerase NeuC complexed with UDP
ComponentsGDP/UDP-N,N'-diacetylbacillosamine 2-epimerase (Hydrolyzing)
KeywordsHYDROLASE / NeuC / UDP N-acetylglucosamine 2-epimerase / TRANSFERASE
Function / homology
Function and homology information


UDP-N,N'-diacetylbacillosamine 2-epimerase (hydrolysing) / UDP-N,N'-diacetylbacillosamine 2-epimerase activity / UDP-N-acetylglucosamine 2-epimerase (hydrolysing) / UDP-N-acetylglucosamine 2-epimerase activity / UDP-N-acetylglucosamine metabolic process / nucleotide binding
Similarity search - Function
UDP-N-acetylglucosamine 2-epimerase,UDP-hydrolysing / UDP-N-acetylglucosamine 2-epimerase WecB-like / UDP-N-acetylglucosamine 2-epimerase domain / UDP-N-acetylglucosamine 2-epimerase
Similarity search - Domain/homology
: / URIDINE-5'-DIPHOSPHATE / GDP/UDP-N,N'-diacetylbacillosamine 2-epimerase (Hydrolyzing)
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.383 Å
AuthorsKo, T.P. / Hsieh, T.J. / Chen, S.C. / Wu, S.C. / Guan, H.H. / Yang, C.H. / Chen, C.J. / Chen, Y.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: The tetrameric structure of sialic acid-synthesizing UDP-GlcNAc 2-epimerase fromAcinetobacter baumannii: A comparative study with human GNE.
Authors: Ko, T.P. / Lai, S.J. / Hsieh, T.J. / Yang, C.S. / Chen, Y.
History
DepositionJun 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 22, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GDP/UDP-N,N'-diacetylbacillosamine 2-epimerase (Hydrolyzing)
B: GDP/UDP-N,N'-diacetylbacillosamine 2-epimerase (Hydrolyzing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6447
Polymers84,6012
Non-polymers1,0435
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-57 kcal/mol
Surface area28630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.879, 147.654, 124.981
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

21A-625-

HOH

31A-701-

HOH

41B-608-

HOH

51B-626-

HOH

61B-659-

HOH

71B-682-

HOH

81B-713-

HOH

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Components

#1: Protein GDP/UDP-N,N'-diacetylbacillosamine 2-epimerase (Hydrolyzing)


Mass: 42300.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: legG, LV38_02406 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A154EJU5, UDP-N,N'-diacetylbacillosamine 2-epimerase (hydrolysing)
#2: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Li
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2 M Li2SO4, 0.1 M Tris-HCl pH 8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→27.95 Å / Num. obs: 32255 / % possible obs: 99.49 % / Redundancy: 6.5 % / Net I/σ(I): 9.22

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZHT

4zht


Resolution: 2.383→27.96 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2108 1620 5.02 %
Rwork0.1713 --
obs0.1733 32251 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.383→27.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5702 0 67 423 6192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045873
X-RAY DIFFRACTIONf_angle_d0.7647954
X-RAY DIFFRACTIONf_dihedral_angle_d15.2463550
X-RAY DIFFRACTIONf_chiral_restr0.048922
X-RAY DIFFRACTIONf_plane_restr0.0041007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3835-2.45350.26141320.20552466X-RAY DIFFRACTION97
2.4535-2.53270.25231270.19982533X-RAY DIFFRACTION100
2.5327-2.62310.26021410.20512525X-RAY DIFFRACTION100
2.6231-2.72810.26591260.19882532X-RAY DIFFRACTION100
2.7281-2.85210.22691390.19142547X-RAY DIFFRACTION100
2.8521-3.00230.23831360.19042540X-RAY DIFFRACTION100
3.0023-3.19020.26951320.19812548X-RAY DIFFRACTION100
3.1902-3.43610.2441390.18682557X-RAY DIFFRACTION100
3.4361-3.78120.20331290.16272564X-RAY DIFFRACTION100
3.7812-4.32660.14751400.14472562X-RAY DIFFRACTION99
4.3266-5.44440.1661370.14872579X-RAY DIFFRACTION99
5.4444-27.96170.23011420.17212678X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 16.7123 Å / Origin y: 13.2566 Å / Origin z: 48.0755 Å
111213212223313233
T0.1933 Å20.0207 Å2-0.0432 Å2-0.1797 Å20.0041 Å2--0.1477 Å2
L1.0162 °2-0.2191 °2-0.447 °2-0.7805 °20.2127 °2--0.4347 °2
S0.0632 Å °0.1296 Å °0.0116 Å °-0.2099 Å °-0.0595 Å °0.1453 Å °-0.1098 Å °-0.0792 Å °0.0021 Å °
Refinement TLS groupSelection details: all

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