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- PDB-5zlr: Structure of NeuC -

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Basic information

Entry
Database: PDB / ID: 5zlr
TitleStructure of NeuC
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 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
: / GDP/UDP-N,N'-diacetylbacillosamine 2-epimerase (Hydrolyzing)
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)85,0656
Polymers84,8592
Non-polymers2064
Water10,287571
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer/tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-75 kcal/mol
Surface area29670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.527, 148.706, 125.723
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-675-

HOH

21A-678-

HOH

31B-714-

HOH

41B-731-

HOH

51B-752-

HOH

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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.: 2
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-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / 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: 297 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→30 Å / Num. obs: 54797 / % possible obs: 99.7 % / Redundancy: 5.2 % / Net I/σ(I): 27.28
Reflection shellResolution: 2.001→2.036 Å

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Processing

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

4zht


Resolution: 2.001→28.95 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.19
RfactorNum. reflection% reflection
Rfree0.2126 2746 5.01 %
Rwork0.1662 --
obs0.1686 54763 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.001→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5784 0 12 572 6368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095898
X-RAY DIFFRACTIONf_angle_d1.0067983
X-RAY DIFFRACTIONf_dihedral_angle_d14.7813572
X-RAY DIFFRACTIONf_chiral_restr0.061922
X-RAY DIFFRACTIONf_plane_restr0.0061023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0015-2.0360.24631500.20512485X-RAY DIFFRACTION98
2.036-2.0730.27681400.1912546X-RAY DIFFRACTION100
2.073-2.11280.26291620.18572573X-RAY DIFFRACTION100
2.1128-2.1560.2371490.17782574X-RAY DIFFRACTION100
2.156-2.20280.2461590.17712555X-RAY DIFFRACTION100
2.2028-2.2540.24091140.17342586X-RAY DIFFRACTION100
2.254-2.31040.19971280.15592606X-RAY DIFFRACTION100
2.3104-2.37280.21881340.15742591X-RAY DIFFRACTION100
2.3728-2.44260.2331380.16972568X-RAY DIFFRACTION100
2.4426-2.52140.24541360.16692595X-RAY DIFFRACTION100
2.5214-2.61150.24061300.17572609X-RAY DIFFRACTION100
2.6115-2.7160.22121120.17682620X-RAY DIFFRACTION100
2.716-2.83950.24161290.17392592X-RAY DIFFRACTION100
2.8395-2.9890.2331340.17742628X-RAY DIFFRACTION100
2.989-3.17610.24211320.18682615X-RAY DIFFRACTION100
3.1761-3.4210.25061210.18112620X-RAY DIFFRACTION100
3.421-3.76460.20261570.16412606X-RAY DIFFRACTION100
3.7646-4.30780.17261620.14222613X-RAY DIFFRACTION100
4.3078-5.42150.18421410.14622668X-RAY DIFFRACTION100
5.4215-28.95340.18121180.16472767X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5070.0102-0.41440.62440.01080.3772-0.0243-0.0086-0.0428-0.20690.0137-0.0468-0.0262-0.021-0.00210.25920.00520.03080.21580.00840.167327.96214.298543.7626
20.727-0.6562-0.55860.63980.25080.45830.20490.7707-0.2885-0.4369-0.53890.2381-0.1526-0.5743-0.23910.41130.0256-0.04810.7987-0.42590.336922.3269-4.374424.8999
30.2911-0.0463-0.31030.5042-0.08820.35590.0001-0.05020.03190.1394-0.02210.3017-0.1574-0.10460.00010.19710.0328-0.02290.2334-0.03840.3579-2.829217.277662.6003
40.402-0.4578-0.10150.48910.09340.39990.0422-0.0005-0.0006-0.066-0.07180.1002-0.0072-0.023-00.18630.0099-0.02690.1960.00310.22088.346615.461854.1654
50.75480.47110.02510.8155-0.19860.23090.2419-0.1640.2934-0.0008-0.14240.0751-0.24320.05240.00020.2525-0.00430.03130.3151-0.06860.33917.902832.372565.7667
60.64760.115-0.14310.40990.01250.35950.095-0.13450.31730.0048-0.0791-0.0243-0.0845-0.0604-0.00010.2789-0.00690.02560.3075-0.07440.395912.639734.403969.1631
70.2881-0.0904-0.40340.4374-0.19330.64780.21410.12140.436-0.1984-0.15950.2259-0.2963-0.17680.01970.29360.0532-0.03350.2292-0.05860.40525.557129.921851.2502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 196 )
2X-RAY DIFFRACTION2chain 'A' and (resid 197 through 379 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 54 )
4X-RAY DIFFRACTION4chain 'B' and (resid 55 through 162 )
5X-RAY DIFFRACTION5chain 'B' and (resid 163 through 229 )
6X-RAY DIFFRACTION6chain 'B' and (resid 230 through 325 )
7X-RAY DIFFRACTION7chain 'B' and (resid 326 through 379 )

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