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- PDB-5dld: Crystal Structure of a UDP-N-acetylglucosamine 2-epimerase from B... -

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Basic information

Entry
Database: PDB / ID: 5dld
TitleCrystal Structure of a UDP-N-acetylglucosamine 2-epimerase from Burkholderia vietnamiensis complexed with UDP-GlcNAc and UDP
ComponentsUDP-N-Acetylglucosamine 2-epimerase
KeywordsISOMERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) / UDP-N-acetylglucosamine 2-epimerase activity / nucleotide binding
Similarity search - Function
UDP-N-acetylglucosamine 2-epimerase WecB-like / UDP-N-acetylglucosamine 2-epimerase domain / UDP-N-acetylglucosamine 2-epimerase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)
Similarity search - Component
Biological speciesBurkholderia vietnamiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a UDP-N-acetylglucosamine 2-epimerase from Burkholderia vietnamiensis complexed with UDP-GlcNAc and UDP
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Dranow, D.M. / Fairman, J.W. / Lorimer, D. / Edwards, T.E.
History
DepositionSep 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0209
Polymers45,6541
Non-polymers1,3668
Water8,215456
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: UDP-N-Acetylglucosamine 2-epimerase
hetero molecules

A: UDP-N-Acetylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,03918
Polymers91,3082
Non-polymers2,73216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7960 Å2
ΔGint-72 kcal/mol
Surface area26590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.000, 81.410, 55.160
Angle α, β, γ (deg.)90.000, 98.030, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-988-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UDP-N-Acetylglucosamine 2-epimerase


Mass: 45653.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia vietnamiensis (bacteria) / Strain: G4 / LMG 22486 / Gene: Bcep1808_4142 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A4JLG9, UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing)

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Non-polymers , 7 types, 464 molecules

#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: BuviA.00061.c.B1.PS02389 at 24.8 mg/ml incubated with 3 mM UDP-N-acetylglucosamine, then then mixed 1:1 with MCSG1(f5): 20% PEG-3350, 0.2 M sodium acetate, cryoprotected with 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 8, 2015 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 87041 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 12.33 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.056 / Χ2: 1.001 / Net I/σ(I): 18.04 / Num. measured all: 360763
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.45-1.493.40.730.5272.2221114659462150.62694.3
1.49-1.530.830.4073.1222642641661160.47895.3
1.53-1.570.90.345425333632760710.39596
1.57-1.620.9340.285.0225007605158170.3296.1
1.62-1.670.9530.2336.1124462590956950.26696.4
1.67-1.730.9670.1947.4423976576855740.22196.6
1.73-1.80.9810.1499.6422771547253090.1797
1.8-1.870.9880.11812.0722017531751530.13496.9
1.87-1.960.9920.09314.8621116509749480.10697.1
1.96-2.050.9950.07418.4220233489347470.08497
2.05-2.160.9960.05623.2119167462545190.06497.7
2.16-2.290.9970.04826.8118303443143300.05597.7
2.29-2.450.9980.04129.7516935408140060.04798.2
2.45-2.650.9980.03633.816121388738170.04298.2
2.65-2.90.9990.03237.9414616352734790.03798.6
2.9-3.240.9990.02941.7613435322631900.03398.9
3.24-3.740.9990.02447.4511755282527970.02899
3.74-4.590.9990.02350.9910003239823790.02699.2
4.59-6.480.9990.02250.487811187818660.02599.4
6.480.9990.02349.773946104910130.02696.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX(dev_2050: ???)refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vgv

1vgv


Resolution: 1.45→27.31 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 14.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.159 4134 4.95 %
Rwork0.1344 79355 -
obs0.1357 83489 93.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.28 Å2 / Biso mean: 19.7916 Å2 / Biso min: 7.39 Å2
Refinement stepCycle: final / Resolution: 1.45→27.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 87 457 3482
Biso mean--21.61 33.96 -
Num. residues----379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073214
X-RAY DIFFRACTIONf_angle_d1.1334404
X-RAY DIFFRACTIONf_chiral_restr0.068502
X-RAY DIFFRACTIONf_plane_restr0.005575
X-RAY DIFFRACTIONf_dihedral_angle_d20.5981189
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4499-1.46640.25641060.20462255236182
1.4664-1.48370.24581230.1982360248382
1.4837-1.50180.21941270.1892363249083
1.5018-1.52080.22691230.16552428255187
1.5208-1.54080.21781170.16392497261487
1.5408-1.56190.2071260.14642507263389
1.5619-1.58420.16751310.13882487261888
1.5842-1.60780.17681270.13192591271890
1.6078-1.6330.16831220.12482549267190
1.633-1.65970.17431300.12482593272391
1.6597-1.68840.1671470.11952582272992
1.6884-1.7190.1631370.12852615275292
1.719-1.75210.16241690.12362584275393
1.7521-1.78790.14871340.12192667280193
1.7879-1.82670.14821480.12272658280694
1.8267-1.86920.16291180.12382687280594
1.8692-1.91590.1631500.12262673282395
1.9159-1.96770.1541710.12972735290696
1.9677-2.02560.14341550.1292690284596
2.0256-2.0910.15661470.12822738288596
2.091-2.16570.16781500.1272728287897
2.1657-2.25240.15571460.12372791293797
2.2524-2.35480.16021270.1262785291298
2.3548-2.47890.1551450.12662778292398
2.4789-2.63410.14091360.13162816295298
2.6341-2.83730.14991470.13792774292199
2.8373-3.12240.1491430.14572844298799
3.1224-3.57340.15971420.14012837297999
3.5734-4.49880.12811350.12492874300999
4.4988-27.31440.16561550.14292869302498

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