[English] 日本語
Yorodumi
- PDB-1a3h: ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHERANS AT 1.6A RESOLUTION -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a3h
TitleENDOGLUCANASE CEL5A FROM BACILLUS AGARADHERANS AT 1.6A RESOLUTION
ComponentsENDOGLUCANASE
KeywordsHYDROLASE / CELLULOSE DEGRADATION / ENDOGLUCANASE / GLYCOSIDE HYDROLASE FAMILY 5
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process / carbohydrate binding / extracellular region
Similarity search - Function
Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily ...Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / 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 speciesBacillus agaradhaerens (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.57 Å
AuthorsDavies, G.J. / Brzozowski, A.M. / Andersen, K. / Schulein, M.
CitationJournal: Biochemistry / Year: 1998
Title: Structure of the Bacillus agaradherans family 5 endoglucanase at 1.6 A and its cellobiose complex at 2.0 A resolution
Authors: Davies, G.J. / Dauter, M. / Brzozowski, A.M. / Bjornvad, M.E. / Andersen, K.V. / Schulein, M.
History
DepositionJan 21, 1998Processing site: BNL
Revision 1.0Mar 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENDOGLUCANASE


Theoretical massNumber of molelcules
Total (without water)33,6541
Polymers33,6541
Non-polymers00
Water7,638424
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.710, 69.570, 77.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ENDOGLUCANASE / CELLULASE


Mass: 33653.746 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus agaradhaerens (bacteria) / Strain: AC13 / Plasmid: THERMAMYL-AMYLASE PROMOTER SYSTEM / Production host: Bacillus subtilis (bacteria) / Strain (production host): PL2306 / References: UniProt: O85465, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE FIRST 3 RESIDUES ARE DISORDERED SO IT STARTS WITH RESIDUE SER 4. THIS THE NATURALLY OCCURRING ...THE FIRST 3 RESIDUES ARE DISORDERED SO IT STARTS WITH RESIDUE SER 4. THIS THE NATURALLY OCCURRING CATALYTIC CORQ DOMAIN AFTER LOSS OF THE CELLULOSE-BINDING DOMAIN(S).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 44 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.8-1.2 Mammonium sulfate1reservoir
215 %(v/v)glycerol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1997 / Details: LONG MIRRORS (MSC)
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.57→15 Å / Num. obs: 222447 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 30.4
Reflection shellResolution: 1.57→1.64 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 8 / Rsym value: 0.196 / % possible all: 98.4
Reflection shell
*PLUS
% possible obs: 98.4 %

-
Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.57→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: ESTIMATED COORDINATE ERROR. ESD FROM SIGMAA (A) : 0.013 LOW RESOLUTION CUTOFF (A) : 15 FIT/AGREEMENT OF MODEL WITH ALL DATA. R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL R VALUE (WORKING ...Details: ESTIMATED COORDINATE ERROR. ESD FROM SIGMAA (A) : 0.013 LOW RESOLUTION CUTOFF (A) : 15 FIT/AGREEMENT OF MODEL WITH ALL DATA. R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL R VALUE (WORKING SET, NO CUTOFF) : 0.12888 FREE R VALUE (NO CUTOFF) : 0.16078
RfactorNum. reflection% reflectionSelection details
Rfree0.17 2074 5 %RANDOM
Rwork0.14 ---
obs-38663 99.8 %-
Displacement parametersBiso mean: 13.8 Å2
Refine analyzeLuzzati d res low obs: 15 Å / Luzzati sigma a obs: 0.01 Å
Refinement stepCycle: LAST / Resolution: 1.57→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2397 0 0 424 2821
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.833
X-RAY DIFFRACTIONp_mcangle_it2.335
X-RAY DIFFRACTIONp_scbond_it3.934
X-RAY DIFFRACTIONp_scangle_it5.466
X-RAY DIFFRACTIONp_plane_restr0.0120.04
X-RAY DIFFRACTIONp_chiral_restr0.110.15
X-RAY DIFFRACTIONp_singtor_nbd0.1740.3
X-RAY DIFFRACTIONp_multtor_nbd0.2250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1850.3
X-RAY DIFFRACTIONp_planar_tor4.97
X-RAY DIFFRACTIONp_staggered_tor12.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.14
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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