[English] 日本語
Yorodumi
- PDB-8va7: Crystal structure of CapGH3a enzyme retrieved from capybara gut m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8va7
TitleCrystal structure of CapGH3a enzyme retrieved from capybara gut metagenome
ComponentsGlycoside hydrolase family 3
KeywordsHYDROLASE / metagenome
Function / homologyDI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION
Function and homology information
Biological speciesgut metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMartins, M.P. / Vieira, P.S. / Morais, M.A.B. / Mandelli, F. / Chinaglia, M. / Lima, E.A. / Murakami, M.T.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2021/09793-0 Brazil
Sao Paulo Research Foundation (FAPESP)2021/04891-3 Brazil
CitationJournal: NPJ Biofilms Microbiomes / Year: 2024
Title: A functionally augmented carbohydrate utilization locus from herbivore gut microbiota fueled by dietary beta-glucans.
Authors: Mandelli, F. / Martins, M.P. / Chinaglia, M. / Lima, E.A. / Morais, M.A.B. / Lima, T.B. / Cabral, L. / Pirolla, R.A.S. / Fuzita, F.J. / Paixao, D.A.A. / Andrade, M.O. / Wolf, L.D. / Vieira, ...Authors: Mandelli, F. / Martins, M.P. / Chinaglia, M. / Lima, E.A. / Morais, M.A.B. / Lima, T.B. / Cabral, L. / Pirolla, R.A.S. / Fuzita, F.J. / Paixao, D.A.A. / Andrade, M.O. / Wolf, L.D. / Vieira, P.S. / Persinoti, G.F. / Murakami, M.T.
History
DepositionDec 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycoside hydrolase family 3
B: Glycoside hydrolase family 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,42910
Polymers165,6082
Non-polymers8208
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.609, 132.867, 99.217
Angle α, β, γ (deg.)90.00, 116.27, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Glycoside hydrolase family 3


Mass: 82804.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) gut metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

-
Non-polymers , 5 types, 163 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M imidazole pH 8.0, PEG8000 (11% v/v)

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.6→47.22 Å / Num. obs: 46772 / % possible obs: 96.2 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.178 / Rrim(I) all: 0.193 / Net I/σ(I): 9.55
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID
2.6-2.761.7876930.7271
2.76-2.951.12572370.7311
2.95-3.180.6767070.8691
3.18-3.480.33961340.9651
3.48-3.890.2346390.9811
3.89-4.490.11649720.9951
4.49-5.490.09541580.9961
5.49-7.710.08133050.9971

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→47.22 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2661 2339 5 %
Rwork0.2223 --
obs0.2245 46772 96.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11096 0 49 155 11300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.42
X-RAY DIFFRACTIONf_dihedral_angle_d10.1574205
X-RAY DIFFRACTIONf_chiral_restr0.041663
X-RAY DIFFRACTIONf_plane_restr0.0032042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.650.45321390.35232642X-RAY DIFFRACTION98
2.65-2.710.34271420.3252710X-RAY DIFFRACTION99
2.71-2.770.36941390.30972632X-RAY DIFFRACTION99
2.77-2.840.36131400.29562655X-RAY DIFFRACTION99
2.84-2.920.36911410.28212683X-RAY DIFFRACTION99
2.92-3.010.34841400.27122653X-RAY DIFFRACTION99
3.01-3.10.33131400.27312662X-RAY DIFFRACTION99
3.1-3.210.32311370.26152594X-RAY DIFFRACTION97
3.21-3.340.31241400.24422664X-RAY DIFFRACTION98
3.34-3.490.28431400.23662663X-RAY DIFFRACTION100
3.5-3.640.30351110.2532105X-RAY DIFFRACTION96
3.7-3.910.25981230.21192330X-RAY DIFFRACTION97
3.91-4.210.20891420.18762690X-RAY DIFFRACTION99
4.21-4.630.22581400.1742665X-RAY DIFFRACTION98
4.64-5.30.1981390.17712659X-RAY DIFFRACTION98
5.31-6.680.23481430.20882715X-RAY DIFFRACTION99

+
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