[English] 日本語
Yorodumi
- PDB-9o4u: Apo-structure of a beta-D-glucuronate dehydratase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9o4u
TitleApo-structure of a beta-D-glucuronate dehydratase
ComponentsBeta-D-glucuronic acid dehydratase
KeywordsLYASE / Beta-D-glucuronate dehydratase
Function / homologyUncharacterised conserved protein UCP014753 / : / Uncharacterized protein conserved in bacteria (DUF2264) / hydrolase activity / DUF2264 domain-containing protein
Function and homology information
Biological speciesBacteroides caccae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsAlvarez, B. / Hettle, A. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)04355 Canada
CitationJournal: To Be Published
Title: Analysis of chondroitin degradation by components of a Bacteroides caccae polysaccharide utilization locus
Authors: Alvarez, B. / Canil, O. / Low, K.E. / Abbott, D.W. / Boraston, A.B.
History
DepositionApr 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-D-glucuronic acid dehydratase
B: Beta-D-glucuronic acid dehydratase
C: Beta-D-glucuronic acid dehydratase
D: Beta-D-glucuronic acid dehydratase


Theoretical massNumber of molelcules
Total (without water)182,3634
Polymers182,3634
Non-polymers00
Water18,1231006
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11880 Å2
ΔGint-60 kcal/mol
Surface area47850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.525, 161.369, 88.610
Angle α, β, γ (deg.)90.000, 95.699, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
Beta-D-glucuronic acid dehydratase


Mass: 45590.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides caccae (bacteria) / Strain: ATCC 43185
Gene: DW190_12820, DW794_00720, DXA49_19590, ERS852494_00337, F2Y31_01635, F2Y35_19060, F2Y36_02775, F2Y39_01210, NXW23_04330
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A174GN40
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1006 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.09 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 220 mM KCl, 24% PEG 3350

-
Data collection

DiffractionMean temperature: 291.15 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.19→20 Å / Num. obs: 76109 / % possible obs: 94.1 % / Redundancy: 2.7 % / Biso Wilson estimate: 31.11 Å2 / CC1/2: 0.968 / Rpim(I) all: 0.046 / Rrim(I) all: 0.083 / Net I/σ(I): 13.2
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3 / Num. unique obs: 76109 / CC1/2: 0.997 / Rpim(I) all: 0.199 / Rrim(I) all: 0.325 / % possible all: 80.7

-
Processing

Software
NameVersionClassification
REFMAC9.0.005refinement
PHENIX1.21.2_5419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→19.84 Å / SU ML: 0.2576 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.2601
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2163 3597 5.11 %
Rwork0.1632 66772 -
obs0.166 70369 91.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.07 Å2
Refinement stepCycle: LAST / Resolution: 2.19→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12270 0 0 1006 13276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006212614
X-RAY DIFFRACTIONf_angle_d0.806617135
X-RAY DIFFRACTIONf_chiral_restr0.04731807
X-RAY DIFFRACTIONf_plane_restr0.0072202
X-RAY DIFFRACTIONf_dihedral_angle_d14.5184556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.220.2761930.18711807X-RAY DIFFRACTION64.02
2.22-2.250.2951220.18952349X-RAY DIFFRACTION84.19
2.25-2.280.29071270.17542375X-RAY DIFFRACTION85.63
2.28-2.320.29531220.17872435X-RAY DIFFRACTION87.15
2.32-2.350.25851350.16552474X-RAY DIFFRACTION88.8
2.35-2.390.23241390.16862491X-RAY DIFFRACTION89.49
2.39-2.430.26491160.17932535X-RAY DIFFRACTION89.89
2.43-2.480.25311470.1782499X-RAY DIFFRACTION91.43
2.48-2.520.25011380.17512573X-RAY DIFFRACTION91.43
2.52-2.570.25441510.18912577X-RAY DIFFRACTION92.73
2.57-2.630.30311310.19862582X-RAY DIFFRACTION93.39
2.63-2.690.27591570.19632642X-RAY DIFFRACTION93.71
2.69-2.760.28011420.19272584X-RAY DIFFRACTION93.74
2.76-2.830.28271380.18992664X-RAY DIFFRACTION94.31
2.83-2.920.24481540.19092576X-RAY DIFFRACTION93.88
2.92-3.010.26851470.19522637X-RAY DIFFRACTION94.57
3.01-3.120.26111290.19732672X-RAY DIFFRACTION94.76
3.12-3.240.26061370.19492689X-RAY DIFFRACTION96.35
3.24-3.390.24831610.18542712X-RAY DIFFRACTION97.32
3.39-3.570.21981380.1642732X-RAY DIFFRACTION96.67
3.57-3.790.20181230.15082727X-RAY DIFFRACTION97.07
3.79-4.080.181370.14392661X-RAY DIFFRACTION95.3
4.08-4.480.15231610.12652682X-RAY DIFFRACTION95.56
4.48-5.120.15941520.12292676X-RAY DIFFRACTION96.35
5.12-6.420.17891390.14582703X-RAY DIFFRACTION96.01
6.42-19.840.13871610.13372718X-RAY DIFFRACTION95.74

+
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