[English] 日本語
Yorodumi
- PDB-5dld: Crystal Structure of a UDP-N-acetylglucosamine 2-epimerase from B... -

+
Open data


ID or keywords:

Loading...

-
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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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)

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more