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

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Basic information

Entry
Database: PDB / ID: 5zlt
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
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 metabolic process / carbohydrate 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: 2.5 Å
AuthorsKo, T.P. / Hsieh, T.J. / Yang, C.S. / Chen, Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology105-2311-B-241-001 Taiwan
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
DepositionMar 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
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 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)
C: GDP/UDP-N,N'-diacetylbacillosamine 2-epimerase (Hydrolyzing)
D: GDP/UDP-N,N'-diacetylbacillosamine 2-epimerase (Hydrolyzing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,7198
Polymers169,7184
Non-polymers1,0004
Water8,899494
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13260 Å2
ΔGint-105 kcal/mol
Surface area54130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.587, 126.144, 145.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 42429.527 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: legG, neuC, CAS83_20140, CUC62_14590, CV949_00455, LV38_02406
Production host: Escherichia coli (E. coli)
References: UniProt: A0A154EJU5, UDP-N,N'-diacetylbacillosamine 2-epimerase (hydrolysing)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2M LiSO4, 0.1M 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: 2.5→30 Å / Num. obs: 54200 / % possible obs: 97.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.6
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.478

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZHT

4zht


Resolution: 2.5→29.591 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.01
RfactorNum. reflection% reflection
Rfree0.2567 2719 5.06 %
Rwork0.2042 --
obs0.2068 53703 96.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11567 0 56 498 12121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311834
X-RAY DIFFRACTIONf_angle_d0.67916023
X-RAY DIFFRACTIONf_dihedral_angle_d14.9187166
X-RAY DIFFRACTIONf_chiral_restr0.0461852
X-RAY DIFFRACTIONf_plane_restr0.0042048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4955-2.54080.37661130.27392375X-RAY DIFFRACTION86
2.5408-2.58970.32291390.25642654X-RAY DIFFRACTION96
2.5897-2.64250.31571460.25262668X-RAY DIFFRACTION98
2.6425-2.69990.30021400.24662683X-RAY DIFFRACTION98
2.6999-2.76270.32641590.23692688X-RAY DIFFRACTION98
2.7627-2.83170.27811540.23672672X-RAY DIFFRACTION98
2.8317-2.90820.30241550.23862694X-RAY DIFFRACTION98
2.9082-2.99370.33521330.22472735X-RAY DIFFRACTION98
2.9937-3.09020.2671550.23192686X-RAY DIFFRACTION98
3.0902-3.20060.2841480.22422697X-RAY DIFFRACTION98
3.2006-3.32850.30291440.22812714X-RAY DIFFRACTION98
3.3285-3.47980.23511450.21872698X-RAY DIFFRACTION98
3.4798-3.6630.25461570.19212662X-RAY DIFFRACTION97
3.663-3.8920.22261480.18392668X-RAY DIFFRACTION95
3.892-4.19170.2091290.16552622X-RAY DIFFRACTION94
4.1917-4.61210.21431250.15962663X-RAY DIFFRACTION94
4.6121-5.27620.2111460.17612675X-RAY DIFFRACTION95
5.2762-6.63510.22371350.20582800X-RAY DIFFRACTION97
6.6351-29.59320.24171480.18842930X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -16.1397 Å / Origin y: 96.4556 Å / Origin z: 109.1732 Å
111213212223313233
T0.1325 Å20.0022 Å2-0.0017 Å2-0.1136 Å2-0.0286 Å2--0.118 Å2
L0.5178 °20.0837 °2-0.0044 °2-0.1612 °20.0437 °2--0.1806 °2
S0.0035 Å °0.0317 Å °-0.0409 Å °-0.0171 Å °0.0254 Å °0.0321 Å °0.01 Å °0.0392 Å °0.0046 Å °
Refinement TLS groupSelection details: all

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