[English] 日本語
Yorodumi
- PDB-8a3h: Cellobiose-derived imidazole complex of the endoglucanase cel5A f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a3h
TitleCellobiose-derived imidazole complex of the endoglucanase cel5A from Bacillus agaradhaerens at 0.97 A resolution
ComponentsPROTEIN (ENDOGLUCANASE)
KeywordsHYDROLASE / CELLULOSE DEGRADATION / GLYCOSIDE HYDROLASE FAMILY 5 / ENDOGLUCANASE / TRANSITION STATE ANALOGUE / LATERAL PROTONATION
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
ACETATE ION / Chem-IDC / Endoglucanase 5A / Endoglucanase B
Similarity search - Component
Biological speciesBacillus agaradhaerens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 0.97 Å
AuthorsVarrot, A. / Schulein, M. / Pipelier, M. / Vasella, A. / Davies, G.J.
CitationJournal: J.Am.Chem.Soc. / Year: 1999
Title: Lateral Protonation of a Glycosidase Inhibitor. Structure of the Bacillus agaradhaerens Cel5A in Complex with a Cellobiose-Derived Imidazole at 0.97 A Resolution
Authors: Varrot, A. / Schulein, M. / Pipelier, M. / Vasella, A. / Davies, G.J.
History
DepositionJan 20, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 21, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_source / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (ENDOGLUCANASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,16011
Polymers33,9981
Non-polymers1,16210
Water8,989499
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.450, 69.880, 77.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein PROTEIN (ENDOGLUCANASE) / CELLULASE


Mass: 33998.023 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 (NCIMB 40482) / Plasmid: THERRAMYL-AMYLASE PROMOTER SYSTEM / Production host: Bacillus subtilis (bacteria) / Strain (production host): PL2306
References: UniProt: P06565, UniProt: O85465*PLUS, cellulase
#4: Sugar ChemComp-IDC / (5R,6R,7R,8S)-7,8-dihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridin-6-yl beta-D-glucopyranoside / 5-HYDROXYMETHYL-5,6,7,8-TETRAHYDRO-IMIDAZO[1,2-A]PYRIDIN-6YL-7,8-DIOL-GLUCOPYRANOSIDE / IMIDAZOLE-DERIVED CELLOBIOSE / (5R,6R,7R,8S)-7,8-dihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridin-6-yl beta-D-glucoside / (5R,6R,7R,8S)-7,8-dihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridin-6-yl D-glucoside / (5R,6R,7R,8S)-7,8-dihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridin-6-yl glucoside


Type: D-saccharide / Mass: 362.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H22N2O9

-
Non-polymers , 4 types, 508 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsTHE THREE FIRST RESIDUES ARE DISORDERED SO SEQUENCE STARTS AT RESIDUE SER A 4 . THIS IS THE ...THE THREE FIRST RESIDUES ARE DISORDERED SO SEQUENCE STARTS AT RESIDUE SER A 4 . THIS IS THE NATURALLY OCCURING CORE DOMAIN AFTER LOSS OF THE CELLULOSE BINDING DOMAIN
Nonpolymer detailsTHE IMIDAZOLE-DERIVED CELLOBIOSIDE IS BOUND IN THE -2 AND -1 SUBSITE. THE IMIDAZOLE RING SITE IN ...THE IMIDAZOLE-DERIVED CELLOBIOSIDE IS BOUND IN THE -2 AND -1 SUBSITE. THE IMIDAZOLE RING SITE IN THE +1 SUBSITE GLYCEROL MOLECULE COMING FROM THE CRYOPROTECTANT SOLUTION
Sequence detailsTHE FIRST 26 RESIDUES IN THE DATABASE CORRESPONDS TO THE PROSEQUENCE. OUR NUMBERING BEGINS AT THE ...THE FIRST 26 RESIDUES IN THE DATABASE CORRESPONDS TO THE PROSEQUENCE. OUR NUMBERING BEGINS AT THE FIRST RESIDUE OBTAINED AFTER CLEAVAGE OF THE PROSEQUENCE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growpH: 5.5
Details: PROTEIN CONCENTRATION 20 MG/ML, 2 M AMMONIUM SULPHATE, 100 MM SODIUM CITRATE PH 5.5, 10% GLYCEROL
Crystal grow
*PLUS
Method: other / Details: Murshudov, G.N., (1997) Acta Cryst., D53, 240.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9076
DetectorDate: Oct 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9076 Å / Relative weight: 1
ReflectionResolution: 0.97→30 Å / Num. obs: 149215 / % possible obs: 93 % / Redundancy: 5.3 % / Biso Wilson estimate: 6.44 Å2 / Rmerge(I) obs: 0.032 / Rsym value: 0.032 / Net I/σ(I): 44.7
Reflection shellResolution: 0.97→1 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.321 / % possible all: 54
Reflection
*PLUS
% possible obs: 93 % / Redundancy: 5.4 %

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
REFMACrefinement
CCP4phasing
RefinementMethod to determine structure: OTHER / Resolution: 0.97→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.118 8085 5 %RANDOM
Rwork0.104 ---
obs-152310 93 %-
Refinement stepCycle: LAST / Resolution: 0.97→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 76 499 2952
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0430.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.9222
X-RAY DIFFRACTIONp_mcangle_it3.5853
X-RAY DIFFRACTIONp_scbond_it3.7552
X-RAY DIFFRACTIONp_scangle_it4.6263
X-RAY DIFFRACTIONp_plane_restr0.0340.04
X-RAY DIFFRACTIONp_chiral_restr0.1240.15
X-RAY DIFFRACTIONp_singtor_nbd0.1690.3
X-RAY DIFFRACTIONp_multtor_nbd0.2560.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.0990.3
X-RAY DIFFRACTIONp_planar_tor6.27
X-RAY DIFFRACTIONp_staggered_tor11.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.820
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.1 / Rfactor Rfree: 0.12 / Rfactor Rwork: 0.1
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_plane_restr / Dev ideal: 0.034

+
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