[English] 日本語
Yorodumi
- PDB-1eqp: EXO-B-(1,3)-GLUCANASE FROM CANDIDA ALBICANS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1eqp
TitleEXO-B-(1,3)-GLUCANASE FROM CANDIDA ALBICANS
ComponentsEXO-B-(1,3)-GLUCANASE
KeywordsHYDROLASE / CANDIDA ALBICANS / EXOGLUCANASE / ALTERNATIVE CODON USAGE
Function / homology
Function and homology information


single-species biofilm formation in or on host organism / glucan metabolic process / glucan 1,3-beta-glucosidase / adhesion of symbiont to host cell / single-species biofilm formation on inanimate substrate / glucan exo-1,3-beta-glucosidase activity / fungal-type cell wall organization / glucan catabolic process / Transferases; Glycosyltransferases; Hexosyltransferases / cell-substrate adhesion ...single-species biofilm formation in or on host organism / glucan metabolic process / glucan 1,3-beta-glucosidase / adhesion of symbiont to host cell / single-species biofilm formation on inanimate substrate / glucan exo-1,3-beta-glucosidase activity / fungal-type cell wall organization / glucan catabolic process / Transferases; Glycosyltransferases; Hexosyltransferases / cell-substrate adhesion / cell adhesion molecule binding / extracellular vesicle / transferase activity / cell surface / extracellular region
Similarity search - Function
: / 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
Glucan 1,3-beta-glucosidase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsCutfield, J.F. / Sullivan, P.A. / Cutfield, S.M.
Citation
Journal: Protein Eng. / Year: 2000
Title: Minor structural consequences of alternative CUG codon usage (Ser for Leu) in Candida albicans exoglucanase.
Authors: Cutfield, J.F. / Sullivan, P.A. / Cutfield, S.M.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: The Structure of the Exo-Beta-(1,3)-Glucanase from Candida albicans in Native and Bound Forms: Relationship Between a Pocket and Groove in Family 5 Glycosyl Hydrolases
Authors: Cutfield, S.M. / Davies, G.J. / Murshudov, G. / Anderson, B.F. / Moody, P.C. / Sullivan, P.A. / Cutfield, J.F.
History
DepositionApr 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EXO-B-(1,3)-GLUCANASE


Theoretical massNumber of molelcules
Total (without water)45,2441
Polymers45,2441
Non-polymers00
Water5,080282
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.10, 65.30, 96.40
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein EXO-B-(1,3)-GLUCANASE


Mass: 45243.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / Strain: ATCC10261 / References: UniProt: P29717, glucan 1,3-beta-glucosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: HEPES BUFFER, CACL2, PEG 8000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Details: Chambers, R.S., (1993) J. Gen. Microbiol., 139, 325., Chambers, R.S., (1993) FEBS Lett., 327, 366.

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 12, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→54 Å / Num. all: 29591 / Num. obs: 26304 / % possible obs: 90.3 % / Observed criterion σ(F): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 14.2
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.103 / % possible all: 48.7
Reflection
*PLUS
Highest resolution: 1.9 Å
Reflection shell
*PLUS
% possible obs: 56.6 % / Mean I/σ(I) obs: 7

-
Processing

Software
NameVersionClassification
ROTAVATAdata reduction
REFMACrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 1.9→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.195 1086 same set as 1CZ1
Rwork0.156 --
all0.154 29282 -
obs0.154 25186 -
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 0 0 282 3507
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d0.025
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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