[English] 日本語
Yorodumi
- PDB-3vho: Y61-gg insertion mutant of Tm-Cellulase 12A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vho
TitleY61-gg insertion mutant of Tm-Cellulase 12A
ComponentsEndo-1,4-beta-glucanase
KeywordsHYDROLASE / jelly roll / cellulose
Function / homology
Function and homology information


cellulase / cellulase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-glucanase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsCheng, Y.-S. / Ko, T.-P. / Guo, R.-T. / Liu, J.-R.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2012
Title: Enhanced activity of Thermotoga maritima cellulase 12A by mutating a unique surface loop
Authors: Cheng, Y.-S. / Ko, T.-P. / Huang, J.W. / Wu, T.H. / Lin, C.Y. / Luo, W. / Li, Q. / Ma, Y. / Huang, C.H. / Wang, A.H. / Liu, J.-R. / Guo, R.-T.
History
DepositionAug 30, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endo-1,4-beta-glucanase
B: Endo-1,4-beta-glucanase


Theoretical massNumber of molelcules
Total (without water)61,4612
Polymers61,4612
Non-polymers00
Water8,719484
1
A: Endo-1,4-beta-glucanase


Theoretical massNumber of molelcules
Total (without water)30,7311
Polymers30,7311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endo-1,4-beta-glucanase


Theoretical massNumber of molelcules
Total (without water)30,7311
Polymers30,7311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.691, 74.333, 168.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Endo-1,4-beta-glucanase / cellulase 12A


Mass: 30730.543 Da / Num. of mol.: 2 / Mutation: Tyr61 replaced by two Gly
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: celA / Plasmid: PET16B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60032, cellulase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 484 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTYR61 REPLACED BY TWO GLY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis-Tris, 0.2M ammonium sulfate, 5% glycerol, 21% PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9732 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2010
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9732 Å / Relative weight: 1
ReflectionResolution: 1.93→25 Å / Num. all: 44574 / Num. obs: 42568 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 23
Reflection shellResolution: 1.93→2 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 8.4 / Num. unique all: 4259 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
Blu-Iceicedata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3AMH

3amh


Resolution: 1.93→25 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2075 -random
Rwork0.175 ---
all0.178 44232 --
obs0.178 41307 93.4 %-
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.93→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4177 0 0 484 4661
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_bond_d0.017
LS refinement shellResolution: 1.93→2 Å / Rfactor Rfree error: 0.05
RfactorNum. reflection% reflection
Rfree0.241 219 -
Rwork0.191 --
obs-4033 92.2 %

+
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