[English] 日本語
Yorodumi
- PDB-9nwf: Structure of an inactive beta-D-glucuronate dehydratase mutant in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9nwf
TitleStructure of an inactive beta-D-glucuronate dehydratase mutant in complex with chondrosine
ComponentsGlucuronate dehydratase
KeywordsLYASE / dehydratase / complex / chondrosine / chondroitin
Function / homologyUncharacterised conserved protein UCP014753 / : / Uncharacterized protein conserved in bacteria (DUF2264) / hydrolase activity / IODIDE ION / DUF2264 domain-containing protein
Function and homology information
Biological speciesBacteroides caccae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBoraston, A.B. / Alvarez, B. / Canil, O.
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. / Abbott, D.W. / Boraston, A.B.
History
DepositionMar 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucuronate dehydratase
B: Glucuronate dehydratase
C: Glucuronate dehydratase
D: Glucuronate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,80535
Polymers183,9574
Non-polymers4,84831
Water7,422412
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18230 Å2
ΔGint-31 kcal/mol
Surface area49190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.543, 105.840, 179.944
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

-
Components

#1: Protein
Glucuronate dehydratase


Mass: 45989.293 Da / Num. of mol.: 4 / Mutation: R285A
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 (E. coli) / References: UniProt: A0A174GN40
#2: Polysaccharide
beta-D-glucopyranuronic acid-(1-3)-2-amino-2-deoxy-beta-D-galactopyranose


Type: oligosaccharide / Mass: 355.295 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpAb1-3DGalpNb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5_2*N][a2122A-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GalpN]{[(3+1)][b-D-GlcpA]{}}LINUCSPDB-CARE
#3: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.25M sodium iodide, 5-13% glycerol, and 8-13% PEG 3350

-
Data collection

DiffractionMean temperature: 100 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: Jan 29, 2025 / Details: VariMaxTM-HF ArcSec
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 58307 / % possible obs: 98.7 % / Redundancy: 4 % / CC1/2: 0.995 / Rpim(I) all: 0.092 / Rrim(I) all: 0.191 / Net I/σ(I): 7.5
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2858 / CC1/2: 0.844 / Rpim(I) all: 0.5 / Rrim(I) all: 0.994 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.96 Å / SU ML: 0.3754 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8321
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2615 2731 5.06 %
Rwork0.1912 51220 -
obs0.1948 53951 91.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.78 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12322 0 123 412 12857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008112819
X-RAY DIFFRACTIONf_angle_d0.962217409
X-RAY DIFFRACTIONf_chiral_restr0.05061857
X-RAY DIFFRACTIONf_plane_restr0.00832222
X-RAY DIFFRACTIONf_dihedral_angle_d16.00294791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.640.3491210.26162200X-RAY DIFFRACTION79.9
2.64-2.690.37031100.25312372X-RAY DIFFRACTION85.35
2.69-2.740.41961400.2542404X-RAY DIFFRACTION87.66
2.74-2.80.34391210.242484X-RAY DIFFRACTION89.86
2.8-2.860.35841250.25092607X-RAY DIFFRACTION92.55
2.86-2.930.33391510.23812590X-RAY DIFFRACTION94.06
2.93-30.35631380.23442605X-RAY DIFFRACTION94.16
3-3.080.30651270.23812626X-RAY DIFFRACTION94.18
3.08-3.170.30481220.21932638X-RAY DIFFRACTION93.97
3.17-3.270.29341430.22872578X-RAY DIFFRACTION93.6
3.27-3.390.3191490.21272636X-RAY DIFFRACTION94.15
3.39-3.520.24921510.18762593X-RAY DIFFRACTION93.65
3.52-3.680.2511210.17972658X-RAY DIFFRACTION94.17
3.68-3.880.22871530.17682599X-RAY DIFFRACTION93.7
3.88-4.120.23411520.16922608X-RAY DIFFRACTION92.84
4.12-4.430.25041300.15532613X-RAY DIFFRACTION92.67
4.43-4.870.18941390.14662617X-RAY DIFFRACTION92.27
4.87-5.560.21241570.16862592X-RAY DIFFRACTION91.48
5.56-6.960.25881510.19332584X-RAY DIFFRACTION90.56
6.96-19.960.22521300.17442616X-RAY DIFFRACTION87.12

+
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