[English] 日本語
Yorodumi
- PDB-4le3: Crystal structure of a GH131 beta-glucanase catalytic domain from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4le3
TitleCrystal structure of a GH131 beta-glucanase catalytic domain from Podospora anserina
ComponentsBeta-glucanase
KeywordsHYDROLASE / glucanase / GH131
Function / homology
Function and homology information


cellulose binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Jelly Rolls - #1160 / Glycoside hydrolase 131, catalytic N-terminal / Glycoside hydrolase 131 catalytic N-terminal domain / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPodospora anserina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsJiang, T. / Chan, H.C. / Huang, C.H. / Ko, T.P. / Huang, T.Y. / Liu, J.R. / Guo, R.T.
CitationJournal: To be Published
Title: Structures of a GH131 beta-Glucanase Catalytic Domain from Podospora anserina in Complex with Cellotriose
Authors: Jiang, T. / Chan, H.C. / Huang, C.H. / Ko, T.P. / Huang, T.Y. / Liu, J.R. / Guo, R.T.
History
DepositionJun 25, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs
Revision 1.2Mar 20, 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: Beta-glucanase
B: Beta-glucanase
C: Beta-glucanase
D: Beta-glucanase


Theoretical massNumber of molelcules
Total (without water)110,8734
Polymers110,8734
Non-polymers00
Water22,9331273
1
A: Beta-glucanase


Theoretical massNumber of molelcules
Total (without water)27,7181
Polymers27,7181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-glucanase


Theoretical massNumber of molelcules
Total (without water)27,7181
Polymers27,7181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-glucanase


Theoretical massNumber of molelcules
Total (without water)27,7181
Polymers27,7181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-glucanase


Theoretical massNumber of molelcules
Total (without water)27,7181
Polymers27,7181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.821, 62.167, 79.154
Angle α, β, γ (deg.)81.61, 75.01, 77.15
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Beta-glucanase


Mass: 27718.361 Da / Num. of mol.: 4 / Fragment: UNP residues 19-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Podospora anserina (fungus) / Plasmid: pET32 Xa/LlC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21trxB(DE3) / References: UniProt: J7K096
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1273 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES, 0.7M LiCl, 33% PEG6K, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 86955 / % possible obs: 96.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.069
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 4.3 / Num. unique all: 8620 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
HKL-2000data collection
OASISmodel building
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
OASISphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→25 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.217 -RANDOM
Rwork0.176 --
all-90811 -
obs-85623 -
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7701 0 0 1273 8974
LS refinement shellResolution: 1.8→1.86 Å /
RfactorNum. reflection
Rfree0.279 -
Rwork0.233 -
obs-7873

+
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