[English] 日本語
Yorodumi
- PDB-8b3y: Native Thermogutta terrifontis endoglucanase catalytic domain wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8b3y
TitleNative Thermogutta terrifontis endoglucanase catalytic domain with a linker at C-terminal from glycoside hydrolase family 5 (TtEnd5A-CDC)
ComponentsEndoglucanase
KeywordsHYDROLASE / endoglucanase / cellulase
Function / homology
Function and homology information


cellulase / cellulase activity / beta-glucosidase activity / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function
: / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermogutta terrifontis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsHussain, N. / Naismith, J.H. / Mikolajek, H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Commonwealth Scholarship Commission (United Kingdom)PKCN-2019-176 United Kingdom
Wellcome Trust100209/Z/12/Z United Kingdom
CitationJournal: Arch.Biochem.Biophys. / Year: 2024
Title: Structural and functional snapshots of a broad-specificity endoglucanase from Thermogutta terrifontis for biomass saccharification.
Authors: Hussain, N. / Mikolajek, H. / Harrison, P.J. / Paterson, N. / Akhtar, M.W. / Sadaf, S. / Naismith, J.H.
History
DepositionSep 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 15, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8914
Polymers38,6031
Non-polymers2883
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-40 kcal/mol
Surface area14050 Å2
Unit cell
Length a, b, c (Å)59.980, 69.520, 81.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Endoglucanase


Mass: 38603.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Initially full length gene was commercially synthesized and then was engineered in the lab to get this truncated mutant
Source: (gene. exp.) Thermogutta terrifontis (bacteria) / Gene: THTE_1171 / Plasmid: TtEnd_CDC_pEHISTEV
Details (production host): pEHISTEV expression vector with inserted gene
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: A0A286RCT9, cellulase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.16 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Well number B2 conditions of LMB screen: 1.9M Ammonium Sulphate, 0.1M MES pH 6.5 + Additive Screen (well number C11 conditions of Grid Screen Salt HR2-248: 2.9 M Sodium malonate pH 5.0) ...Details: Well number B2 conditions of LMB screen: 1.9M Ammonium Sulphate, 0.1M MES pH 6.5 + Additive Screen (well number C11 conditions of Grid Screen Salt HR2-248: 2.9 M Sodium malonate pH 5.0) TtEnd5A CD-C variant = 10.6 mg/ml. 10x Cellobiose (100 uM)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.25→48.26 Å / Num. obs: 93566 / % possible obs: 99 % / Redundancy: 12 % / Biso Wilson estimate: 16.21 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.017 / Rrim(I) all: 0.059 / Net I/σ(I): 15.7
Reflection shellResolution: 1.25→1.28 Å / Redundancy: 5.4 % / Rmerge(I) obs: 2.076 / Num. unique obs: 6204 / CC1/2: 0.348 / Rpim(I) all: 0.952 / Rrim(I) all: 2.183 / % possible all: 90.4

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
Coot0.9.6model building
MOLREPphasing
PDB-REDOrefinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8AG9

8ag9


Resolution: 1.25→48.26 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.459 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.16052 4586 4.9 %RANDOM
Rwork0.13679 ---
obs0.13793 88862 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å2-0 Å2
2---1.2 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.25→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2732 0 15 236 2983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0172883
X-RAY DIFFRACTIONr_bond_other_d0.0010.0192604
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.8213943
X-RAY DIFFRACTIONr_angle_other_deg1.192.6095976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0835346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.32520.865185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52615441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2371529
X-RAY DIFFRACTIONr_chiral_restr0.090.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023313
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02741
X-RAY DIFFRACTIONr_mcbond_it1.6921.771354
X-RAY DIFFRACTIONr_mcbond_other1.681.7661353
X-RAY DIFFRACTIONr_mcangle_it1.9812.6641695
X-RAY DIFFRACTIONr_mcangle_other1.9842.6681696
X-RAY DIFFRACTIONr_scbond_it2.3992.1131529
X-RAY DIFFRACTIONr_scbond_other2.3872.1091517
X-RAY DIFFRACTIONr_scangle_other2.9733.0492226
X-RAY DIFFRACTIONr_long_range_B_refined3.07121.5253333
X-RAY DIFFRACTIONr_long_range_B_other2.92321.2053296
X-RAY DIFFRACTIONr_rigid_bond_restr2.31935487
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.486 296 -
Rwork0.503 5868 -
obs--89.46 %

+
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