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- PDB-6vlb: Crystal structure of ligand-free UDP-GlcNAc 2-epimerase from Neis... -

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Basic information

Entry
Database: PDB / ID: 6vlb
TitleCrystal structure of ligand-free UDP-GlcNAc 2-epimerase from Neisseria meningitidis
ComponentsUDP-N-acetylglucosamine 2-epimerase
KeywordsISOMERASE / Epimerase UDP-GlcNAc UDP-ManNAc UDP-GlcNAc 2-epimerase
Function / homologyUDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) / UDP-N-acetylglucosamine 2-epimerase WecB-like / UDP-N-acetylglucosamine 2-epimerase domain / UDP-N-acetylglucosamine 2-epimerase / UDP-N-acetylglucosamine 2-epimerase activity / capsule polysaccharide biosynthetic process / UDP-N-acetylglucosamine 2-epimerase
Function and homology information
Biological speciesNeisseria meningitidis serogroup A / serotype 4A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsFisher, A.J. / Hurlburt, N.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM094523 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Structural characterization of a nonhydrolyzing UDP-GlcNAc 2-epimerase from Neisseria meningitidis serogroup A.
Authors: Hurlburt, N.K. / Guan, J. / Ong, H. / Yu, H. / Chen, X. / Fisher, A.J.
History
DepositionJan 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine 2-epimerase
B: UDP-N-acetylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8065
Polymers85,6982
Non-polymers1083
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Homology to E. coli Enzyme.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-43 kcal/mol
Surface area31090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.550, 49.510, 81.220
Angle α, β, γ (deg.)90.000, 90.930, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-605-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 1 - 370 / Label seq-ID: 1 - 370

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein UDP-N-acetylglucosamine 2-epimerase / UDP-GlcNAc 2-epimerase


Mass: 42849.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup A / serotype 4A (strain Z2491) (bacteria)
Strain: Z2491 / Gene: sacA, NMA0199 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0U1RGY0, UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.51 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 50% (v/v) PEG-200, 100 mM phosphate-citrate, pH 4.2, and 200 mM NaCl.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 71340 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.46 % / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.077 / Net I/σ(I): 10.8
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.65 / Num. unique obs: 19336 / CC1/2: 0.89 / Rrim(I) all: 0.498 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSVERSION September 26, 2012data reduction
XSCALEVERSION July 4, 2012data scaling
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F6D

1f6d


Resolution: 1.85→36.42 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.415 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.125
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2157 3593 5 %RANDOM
Rwork0.1824 ---
obs0.1841 67746 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 133.63 Å2 / Biso mean: 34.714 Å2 / Biso min: 14.37 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å2-0.14 Å2
2--2.27 Å20 Å2
3----1.07 Å2
Refinement stepCycle: final / Resolution: 1.85→36.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5863 0 6 424 6293
Biso mean--49.49 43.06 -
Num. residues----743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136015
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175743
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.6418180
X-RAY DIFFRACTIONr_angle_other_deg1.4361.56613407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1775751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50124.161274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.238151101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8151522
X-RAY DIFFRACTIONr_chiral_restr0.0750.2843
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026544
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021090
Refine LS restraints NCS

Ens-ID: 1 / Number: 11666 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 279 -
Rwork0.247 4873 -
all-5152 -
obs--96.97 %

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