[English] 日本語
Yorodumi
- PDB-8sxw: X-ray crystal structure of UDP- 2,3-diacetamido-2,3-dideoxy-glucu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8sxw
TitleX-ray crystal structure of UDP- 2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase from Thermus thermophilus strain HB27, D98N mutation, apo structure at pH 6
ComponentsUDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase
KeywordsISOMERASE / lipopolysaccharide / O-antigen / 2-epimerase
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
UDP-N-acetylglucosamine 2-epimerase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKroft, C.W. / Thoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM134643 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural analysis of a bacterial UDP-sugar 2-epimerase reveals the active site architecture before and after catalysis.
Authors: Thoden, J.B. / McKnight, J.O. / Kroft, C.W. / Jast, J.D.T. / Holden, H.M.
History
DepositionMay 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase
B: UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase
C: UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase
D: UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,5667
Polymers164,4734
Non-polymers943
Water20,0151111
1
A: UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase
B: UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2954
Polymers82,2362
Non-polymers582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-28 kcal/mol
Surface area29950 Å2
MethodPISA
2
C: UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase
D: UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2723
Polymers82,2362
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-21 kcal/mol
Surface area30820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.327, 85.340, 86.535
Angle α, β, γ (deg.)108.23, 110.06, 97.10
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase


Mass: 41118.145 Da / Num. of mol.: 4 / Mutation: D98N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Strain: ATCC BAA-163 / DSM 7039 / HB27 / Gene: TT_C0285 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q72KY0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 18-22% pentaerythritol propoxylate (5/4 PO/OH), 100 mM MES (pH 6)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Mar 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 139158 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.055 / Net I/σ(I): 16.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 19632 / Rsym value: 0.35 / % possible all: 89.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→41.72 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.505 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22449 7133 5.1 %RANDOM
Rwork0.1785 ---
obs0.18084 132025 94.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.849 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20.01 Å2
2---0.01 Å20.01 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→41.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11343 0 3 1111 12457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01211690
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611351
X-RAY DIFFRACTIONr_angle_refined_deg1.421.6515884
X-RAY DIFFRACTIONr_angle_other_deg0.4831.57326051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14551479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.8595107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.768102015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.21801
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213902
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022682
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2872.4165817
X-RAY DIFFRACTIONr_mcbond_other2.2872.4165817
X-RAY DIFFRACTIONr_mcangle_it3.4784.3317275
X-RAY DIFFRACTIONr_mcangle_other3.4774.3317276
X-RAY DIFFRACTIONr_scbond_it3.2052.9155873
X-RAY DIFFRACTIONr_scbond_other3.2052.9165874
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1565.1328592
X-RAY DIFFRACTIONr_long_range_B_refined6.95328.2413478
X-RAY DIFFRACTIONr_long_range_B_other6.86626.6713143
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.843 Å
RfactorNum. reflection% reflection
Rfree0.323 445 -
Rwork0.316 8270 -
obs--79.65 %

+
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://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