[English] 日本語
Yorodumi
- PDB-1ut9: Structural Basis for the Exocellulase Activity of the Cellobiohyd... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ut9
TitleStructural Basis for the Exocellulase Activity of the Cellobiohydrolase CbhA from C. thermocellum
ComponentsCELLULOSE 1,4-BETA-CELLOBIOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / FAMILY 9 / CELLOBIOHYDROLASE
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase activity / cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily ...Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.1 Å
AuthorsSchubot, F.D. / Kataeva, I.A. / Chang, J. / Shah, A.K. / Ljungdahl, L.G. / Rose, J.P. / Wang, B.C.
CitationJournal: Biochemistry / Year: 2004
Title: Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum.
Authors: Schubot, F.D. / Kataeva, I.A. / Chang, J. / Shah, A.K. / Ljungdahl, L.G. / Rose, J.P. / Wang, B.C.
History
DepositionDec 4, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Experimental preparation / Source and taxonomy
Category: citation / diffrn_detector ...citation / diffrn_detector / diffrn_radiation / entity_src_gen / exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn_detector.detector / _diffrn_detector.type / _diffrn_radiation.pdbx_diffrn_protocol / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _exptl_crystal_grow.method
Revision 1.4May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CELLULOSE 1,4-BETA-CELLOBIOSIDASE


Theoretical massNumber of molelcules
Total (without water)68,6081
Polymers68,6081
Non-polymers00
Water15,493860
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.546, 75.760, 137.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein CELLULOSE 1,4-BETA-CELLOBIOSIDASE / CELLOBIOHYDROLASE CBHA / EXOGLUCANASE / EXOCELLOBIOHYDROLASE / 1 / 4-BETA-CELLOBIOHYDROLASE


Mass: 68608.016 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 208-816
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Plasmid: PET-21B(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6RSN8*PLUS, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 860 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57 %
Crystal growMethod: batch mode / pH: 8.5 / Details: 20% PEG4000, 0.2M (NH4)2SO4, 0.1M TRIS, PH 7.0
Crystal grow
*PLUS
Temperature: 273 K / pH: 8.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
225 mMTris-HCl1droppH8.5
30.2 M1dropNaCl
420 %PEG40001reservoir
50.2 Mammonium sulfate1reservoir
60.1 MTris1reservoirpH7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: RIGAKU HI RES OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→69 Å / Num. obs: 41182 / % possible obs: 92 % / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3 / % possible all: 66
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 69 Å / % possible obs: 91.6 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 65.9 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 3.1

-
Processing

Software
NameClassification
REFMACrefinement
PROTEUMdata reduction
PROTEUMdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.1→69.01 Å / SU B: 3.621 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.149
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PLEASE NOTE THAT THIS ENTRY CONTAINS ATOMS REFINED WITH 0.00 OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.18553 2190 5 %RANDOM
Rwork0.14732 ---
obs0.14928 41182 93.82 %-
Displacement parametersBiso mean: 17.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--0.31 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.1→69.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4809 0 0 860 5669
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 69 Å / Rfactor Rfree: 0.185 / Rfactor Rwork: 0.147
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.008
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.381

+
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://pdbjlvh1.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