[English] 日本語
Yorodumi
- PDB-8b0e: Crystal structure of beta-glucuronidase from Acidobacterium capsu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8b0e
TitleCrystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with covalent inhibitor VB158
Componentsbeta-glucuronidase from Acidobacterium capsulatum
KeywordsHYDROLASE / b-glucuronidase
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / membrane
Similarity search - Function
Beta-glucuronidase, C-terminal / Glycosyl hydrolase family 79 C-terminal beta domain / Glycoside hydrolase, family 79 / Glycosyl hydrolase family 79, N-terminal domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-OV3 / Beta-glucuronidase C-terminal domain-containing protein
Similarity search - Component
Biological speciesAcidobacterium capsulatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsArmstrong, Z. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Chemmedchem / Year: 2023
Title: 4-O-Substituted Glucuronic Cyclophellitols are Selective Mechanism-Based Heparanase Inhibitors.
Authors: Borlandelli, V. / Armstrong, Z. / Nin-Hill, A. / Codee, J.D.C. / Raich, L. / Artola, M. / Rovira, C. / Davies, G.J. / Overkleeft, H.S.
History
DepositionSep 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 1, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: beta-glucuronidase from Acidobacterium capsulatum
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1462
Polymers50,8151
Non-polymers3311
Water5,981332
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.829, 44.476, 137.577
Angle α, β, γ (deg.)90.000, 97.629, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11AAA-652-

HOH

21AAA-827-

HOH

-
Components

#1: Protein beta-glucuronidase from Acidobacterium capsulatum


Mass: 50814.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidobacterium capsulatum (bacteria)
Strain: ATCC 51196 / DSM 11244 / BCRC 80197 / JCM 7670 / NBRC 15755 / NCIMB 13165 / 161
Gene: ACP_2665 / Production host: Escherichia coli (E. coli) / References: UniProt: C1F2K5
#2: Chemical ChemComp-OV3 / (1~{S},2~{R},3~{R},4~{S},6~{S})-3,4,6-tris(oxidanyl)-2-[2-[2,2,2-tris(fluoranyl)ethanoylamino]ethoxy]cyclohexane-1-carboxylic acid


Mass: 331.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16F3NO7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.5 M AmSO4 1 M LiSO4 0.1 M Trisodium Citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.55→39.21 Å / Num. obs: 70791 / % possible obs: 96.8 % / Redundancy: 5.8 % / CC1/2: 0.966 / Net I/σ(I): 2.9
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 3423 / CC1/2: 0.616

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5g0m

5g0m


Resolution: 1.55→39.21 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.836 / SU ML: 0.096 / Cross valid method: FREE R-VALUE / ESU R: 0.094 / ESU R Free: 0.095
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2519 3509 4.963 %
Rwork0.2198 67196 -
all0.221 --
obs-70705 96.362 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.243 Å2
Baniso -1Baniso -2Baniso -3
1--1.158 Å2-0 Å20.444 Å2
2--1.952 Å2-0 Å2
3----0.881 Å2
Refinement stepCycle: LAST / Resolution: 1.55→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3341 0 22 332 3695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133491
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173116
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.6494761
X-RAY DIFFRACTIONr_angle_other_deg1.3991.5717219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5945445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.26821.844179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18215505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0631522
X-RAY DIFFRACTIONr_chiral_restr0.0750.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024025
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02778
X-RAY DIFFRACTIONr_nbd_refined0.2020.2605
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.22765
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21670
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21482
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2242
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1530.211
X-RAY DIFFRACTIONr_nbd_other0.1650.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1640.220
X-RAY DIFFRACTIONr_mcbond_it1.4911.9241777
X-RAY DIFFRACTIONr_mcbond_other1.4911.9231776
X-RAY DIFFRACTIONr_mcangle_it2.3312.8792223
X-RAY DIFFRACTIONr_mcangle_other2.332.8792224
X-RAY DIFFRACTIONr_scbond_it1.9832.1281714
X-RAY DIFFRACTIONr_scbond_other1.9792.1251710
X-RAY DIFFRACTIONr_scangle_it3.0353.1242538
X-RAY DIFFRACTIONr_scangle_other3.0363.1212536
X-RAY DIFFRACTIONr_lrange_it4.75923.0273865
X-RAY DIFFRACTIONr_lrange_other4.66922.6583793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.3132560.3164850X-RAY DIFFRACTION94.731
1.59-1.6340.3152620.2994688X-RAY DIFFRACTION94.8094
1.634-1.6810.3342230.2894666X-RAY DIFFRACTION95.5629
1.681-1.7330.3282200.2844486X-RAY DIFFRACTION95.2246
1.733-1.790.3132240.2744406X-RAY DIFFRACTION95.6216
1.79-1.8520.312440.264211X-RAY DIFFRACTION95.8271
1.852-1.9220.2721850.2424134X-RAY DIFFRACTION96.0205
1.922-2.0010.2772180.2283929X-RAY DIFFRACTION95.9732
2.001-2.090.2592190.2313793X-RAY DIFFRACTION96.4887
2.09-2.1920.271980.2173668X-RAY DIFFRACTION96.6742
2.192-2.310.2921610.2143508X-RAY DIFFRACTION97.0635
2.31-2.450.2551920.2093278X-RAY DIFFRACTION96.6843
2.45-2.6190.2281670.2013116X-RAY DIFFRACTION97.5342
2.619-2.8280.2241530.1942921X-RAY DIFFRACTION97.7114
2.828-3.0980.2651280.2152721X-RAY DIFFRACTION98.2753
3.098-3.4630.21200.1992473X-RAY DIFFRACTION98.4434
3.463-3.9970.1891030.1752214X-RAY DIFFRACTION98.6377
3.997-4.8920.2121090.191834X-RAY DIFFRACTION97.7364
4.892-6.9040.24770.2061460X-RAY DIFFRACTION99.0335
6.904-39.210.243500.232840X-RAY DIFFRACTION98.1257

+
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