[English] 日本語
Yorodumi
- PDB-4a3h: 2',4' DINITROPHENYL-2-DEOXY-2-FLURO-B-D-CELLOBIOSIDE COMPLEX OF T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4a3h
Title2',4' DINITROPHENYL-2-DEOXY-2-FLURO-B-D-CELLOBIOSIDE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS AT 1.6 A RESOLUTION
ComponentsPROTEIN (ENDOGLUCANASE)
KeywordsHYDROLASE / CELLULOSE DEGRADATION / ENDOGLUCANASE / GLYCOSIDE HYDROLASE FAMILY 5 / MICHAELIS COMPLEX. SKEW-BOAT / DISTORTION
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
Chem-DCB / Endoglucanase 5A / Endoglucanase B
Similarity search - Component
Biological speciesBacillus agaradhaerens (bacteria)
MethodX-RAY DIFFRACTION / ISOMORPHOUS WITH NATIVE STRUCTURE / Resolution: 1.65 Å
AuthorsDavies, G.J. / Brzozowski, A.M. / Andersen, K. / Schulein, M. / Mackenzie, L. / Withers, S.G.
Citation
Journal: Biochemistry / Year: 1998
Title: Snapshots along an enzymatic reaction coordinate: analysis of a retaining beta-glycoside hydrolase.
Authors: Davies, G.J. / Mackenzie, L. / Varrot, A. / Dauter, M. / Brzozowski, A.M. / Schulein, M. / Withers, S.G.
#1: Journal: 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
DepositionJul 22, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 23, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (ENDOGLUCANASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5082
Polymers33,9981
Non-polymers5101
Water7,512417
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 PROTEIN (ENDOGLUCANASE) / E.C.3.2.1.4 HYDROLASE / CELLULASE


Mass: 33998.023 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN ONLY
Source method: isolated from a genetically manipulated source
Details: THIS IS A COMPLEX WITH 2,4-DINITROPHENYL, 2-FLUOROCELLOBIOSEOUND IN THE -1, -2 AND +1 SITES OF THE ENZYME
Source: (gene. exp.) Bacillus agaradhaerens (bacteria) / Strain: AC13 (NCIMB 40482) / Plasmid: THERMAMYL-AMYLASE PROMOTER SYSTEM / Production host: Bacillus subtilis (bacteria) / Strain (production host): PL2306
References: UniProt: P06565, UniProt: O85465*PLUS, cellulase
#2: Chemical ChemComp-DCB / 2,4-DINITROPHENYL-2-DEOXY-2-FLUORO-BETA-D-CELLOBIOSIDE / 2',4'-DINITROPHENYL-2DEOXY-2-FLURO-B-D-CELLOBIOSIDE


Mass: 510.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H23FN2O14
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCEL5A IS A MEMBER OF GLYCOSIDE HYDROLASE FAMILY 5 THIS IS ONE OF THE GH-A CLAN MEMBERS
Nonpolymer detailsHET ID DCB THE CELLOBIOSE MOEITY IS BOUND IN THE -2 AND -1 SUBSITES WITH THE UNHYDROLYSED DNP GROUP IN +1.
Sequence detailsREFERENCE: SEQUENCE NOT DEPOSITED.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growpH: 5.5
Details: PROTEIN (20MGML-1) WAS CRYSTALLISED FROM 1.0M AMMONIUM SULPHATE AS BOTH BUFFER AND PRECIPITANT AT PH 4.5 IN THE PRESENCE OF 15% (W/V) GLYCEROL, pH 5.5 THIS STRUCTURE WAS OBTAINED BY SOAKING ...Details: PROTEIN (20MGML-1) WAS CRYSTALLISED FROM 1.0M AMMONIUM SULPHATE AS BOTH BUFFER AND PRECIPITANT AT PH 4.5 IN THE PRESENCE OF 15% (W/V) GLYCEROL, pH 5.5 THIS STRUCTURE WAS OBTAINED BY SOAKING THE CRYSTALS IN 10MM 2",4" DINITROPHENYL-2-DEOXY-2-FLUORO-B-D-CELLOBIOSIDE FOR 12 H PRIOR TO DATA COLLECTION.
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion, hanging drop / Details: Davies, G.J., (1998) Biochemistry, 37, 1926.
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 RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1997 / Details: LONG FOCUSSING MIRRORS (MSC)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 35964 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 22.6
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 13.4 / Rsym value: 0.176 / % possible all: 99.9
Reflection shell
*PLUS
% possible obs: 99.8 %

-
Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: ISOMORPHOUS WITH NATIVE STRUCTURE
Resolution: 1.65→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.172 1832 5 %RANDOM
Rwork0.142 ---
obs-35910 99.9 %-
Displacement parametersBiso mean: 15.8 Å2
Refinement stepCycle: LAST / Resolution: 1.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 35 417 2829
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_it1.63
X-RAY DIFFRACTIONp_mcangle_it2.15
X-RAY DIFFRACTIONp_scbond_it3.14
X-RAY DIFFRACTIONp_scangle_it4.56
X-RAY DIFFRACTIONp_plane_restr0.0120.04
X-RAY DIFFRACTIONp_chiral_restr0.130.11
X-RAY DIFFRACTIONp_singtor_nbd0.1740.3
X-RAY DIFFRACTIONp_multtor_nbd0.2450.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1690.3
X-RAY DIFFRACTIONp_planar_tor4.57
X-RAY DIFFRACTIONp_staggered_tor13.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.14
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_chiral_restr0.11
X-RAY DIFFRACTIONp_mcbond_it1.6
X-RAY DIFFRACTIONp_scbond_it3.1
X-RAY DIFFRACTIONp_mcangle_it2.1
X-RAY DIFFRACTIONp_scangle_it4.5

+
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