[English] 日本語
Yorodumi
- PDB-2vuy: Crystal structure of Glycogen Debranching exzyme TreX from Sulfol... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vuy
TitleCrystal structure of Glycogen Debranching exzyme TreX from Sulfolobus solfatarius
ComponentsGLYCOGEN OPERON PROTEIN GLGX
KeywordsHYDROLASE / GLYCOSIDASE / GLYCOSYL HYDROLASE
Function / homology
Function and homology information


: / glycogen catabolic process / aminopeptidase activity / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycogen debranching enzyme, GlgX type / Glycogen debranching enzyme GlgX/isoamylase, N-terminal Early set domain / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha amylase, C-terminal all-beta domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...Glycogen debranching enzyme, GlgX type / Glycogen debranching enzyme GlgX/isoamylase, N-terminal Early set domain / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha amylase, C-terminal all-beta domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Glycogen debranching enzyme
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSong, H.-N. / Yoon, S.-M. / Cha, H.-J. / Park, K.-H. / Woo, E.-J.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural Insight Into the Bifunctional Mechanism of the Glycogen-Debranching Enzyme Trex from the Archaeon Sulfolobus Solfataricus.
Authors: Woo, E. / Lee, S. / Cha, H. / Park, J. / Yoon, S. / Song, H. / Park, K.
History
DepositionJun 2, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Structure summary / Version format compliance
Revision 1.2Apr 1, 2015Group: Database references
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD", "BD" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD", "BD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLYCOGEN OPERON PROTEIN GLGX
B: GLYCOGEN OPERON PROTEIN GLGX


Theoretical massNumber of molelcules
Total (without water)166,3642
Polymers166,3642
Non-polymers00
Water00
1
A: GLYCOGEN OPERON PROTEIN GLGX
B: GLYCOGEN OPERON PROTEIN GLGX

A: GLYCOGEN OPERON PROTEIN GLGX
B: GLYCOGEN OPERON PROTEIN GLGX

A: GLYCOGEN OPERON PROTEIN GLGX
B: GLYCOGEN OPERON PROTEIN GLGX


Theoretical massNumber of molelcules
Total (without water)499,0916
Polymers499,0916
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area19170 Å2
ΔGint-55.5 kcal/mol
Surface area141610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.633, 203.633, 89.428
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

-
Components

#1: Protein GLYCOGEN OPERON PROTEIN GLGX / GLYCOGEN DEBRANCHING ENZYME / TREX


Mass: 83181.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DISULFIDE BOND BETWEEN A254 AND A261, A505 AND A519, B254 AND B261, B505 AND B519
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P95868, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.4 % / Description: NONE
Crystal growpH: 9.5 / Details: 16% PEG 8000, 0.2M NACL, 0.1 CHESS BUFFER(PH9.5)

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 39857 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.24 / % possible all: 95.8

-
Processing

SoftwareName: PHASER / Classification: phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BF2

1bf2


Resolution: 3→29.86 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2004 5 %RANDOM
Rwork0.206 ---
obs-39857 --
Displacement parametersBiso mean: 35.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2---0.7 Å20 Å2
3---1.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 3→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11634 0 0 0 11634
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.006
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.2
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d24.7
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d1.28
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
Rfactor% reflection
Rfree0.346 5.2 %
Rwork0.309 -
obs-86.6 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

+
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