[English] 日本語
Yorodumi
- PDB-5e0c: Structural Insight of a Trimodular Halophilic Cellulase with a Fa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5e0c
TitleStructural Insight of a Trimodular Halophilic Cellulase with a Family 46 Carbohydrate-Binding Module
ComponentsCellulase
KeywordsHYDROLASE / cellulase / carbohydrate-binding module / substrate binding cleft / halophilic
Function / homology
Function and homology information


cellulase activity / cellulose catabolic process
Similarity search - Function
Endoglucanase B, carbohydrate binding domain / Carbohydrate binding domain / Glycoside hydrolase, family 5, endoglucanase B / Carbohydrate binding X2 domain / Carbohydrate binding domain X2 / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases ...Endoglucanase B, carbohydrate binding domain / Carbohydrate binding domain / Glycoside hydrolase, family 5, endoglucanase B / Carbohydrate binding X2 domain / Carbohydrate binding domain X2 / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus sp. BG-CS10 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.351 Å
AuthorsZhang, H.D. / Zhang, H.J.
CitationJournal: To Be Published
Title: Structural Insight of a Trimodular Halophilic Cellulase with a Family 46 Carbohydrate-Binding Module
Authors: Zhang, H.D. / Zhang, H.J.
History
DepositionSep 28, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cellulase


Theoretical massNumber of molelcules
Total (without water)61,6541
Polymers61,6541
Non-polymers00
Water8,305461
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21280 Å2
Unit cell
Length a, b, c (Å)120.143, 120.143, 205.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-808-

HOH

21A-989-

HOH

-
Components

#1: Protein Cellulase / / CelB


Mass: 61654.430 Da / Num. of mol.: 1 / Fragment: UNP residues 34-569
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. BG-CS10 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: D4P8C6, cellulase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.06 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.0 M ammonium sulfate, 5% (v/v) 2-propanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.351→65.451 Å / Num. obs: 30948 / % possible obs: 98.2 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.4
Reflection shellResolution: 2.351→2.435 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.5 / % possible all: 95.5

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 5000000000 / Resolution: 2.351→65.451 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2315 1440 4.65 %
Rwork0.1788 --
obs0.1812 30943 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.351→65.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4312 0 0 461 4773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074430
X-RAY DIFFRACTIONf_angle_d0.9856032
X-RAY DIFFRACTIONf_dihedral_angle_d13.41559
X-RAY DIFFRACTIONf_chiral_restr0.038635
X-RAY DIFFRACTIONf_plane_restr0.004801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3509-2.43490.35231480.24722794X-RAY DIFFRACTION95
2.4349-2.53240.3011430.23492973X-RAY DIFFRACTION100
2.5324-2.64760.27491440.23022962X-RAY DIFFRACTION100
2.6476-2.78720.25791670.21432939X-RAY DIFFRACTION99
2.7872-2.96190.29621410.20632971X-RAY DIFFRACTION99
2.9619-3.19060.20871420.18942942X-RAY DIFFRACTION99
3.1906-3.51160.22141460.16832954X-RAY DIFFRACTION98
3.5116-4.01970.21781220.14942975X-RAY DIFFRACTION97
4.0197-5.06410.17561520.13762944X-RAY DIFFRACTION97
5.0641-65.47620.21551350.17563049X-RAY DIFFRACTION94

+
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