[English] 日本語
Yorodumi
- PDB-2pri: BINDING OF 2-DEOXY-GLUCOSE-6-PHOSPHATE TO GLYCOGEN PHOSPHORYLASE B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pri
TitleBINDING OF 2-DEOXY-GLUCOSE-6-PHOSPHATE TO GLYCOGEN PHOSPHORYLASE B
ComponentsGLYCOGEN PHOSPHORYLASE B
KeywordsTRANSFERASE / GLYCOGEN PHOSPHORYLASE
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding
Similarity search - Function
Glycosyl transferase, family 35 / Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Carbohydrate phosphorylase / Phosphorylase pyridoxal-phosphate attachment site. / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-deoxy-6-O-phosphono-alpha-D-glucopyranose / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsOikonomakos, N.G. / Zographos, S.E. / Johnson, L.N. / Papageorgiou, A.C. / Acharya, K.R.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: The binding of 2-deoxy-D-glucose 6-phosphate to glycogen phosphorylase b: kinetic and crystallographic studies.
Authors: Oikonomakos, N.G. / Zographos, S.E. / Johnson, L.N. / Papageorgiou, A.C. / Acharya, K.R.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallographic Binding Studies on the Allosteric Inhibitor Glucose-6- Phosphate to T State Glycogen Phosphorylase B
Authors: Johnson, L.N. / Snape, P. / Martin, J.L. / Acharya, K.R. / Barford, D. / Oikonomakos, N.G.
History
DepositionDec 11, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Dec 14, 1998Provider: repository / Type: Initial release
SupersessionDec 16, 1998ID: 1PRI
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 29, 2012Group: Non-polymer description
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLYCOGEN PHOSPHORYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7823
Polymers97,2911
Non-polymers4912
Water4,594255
1
A: GLYCOGEN PHOSPHORYLASE B
hetero molecules

A: GLYCOGEN PHOSPHORYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,5656
Polymers194,5822
Non-polymers9834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7380 Å2
ΔGint-32 kcal/mol
Surface area58600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.500, 128.500, 116.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

-
Components

#1: Protein GLYCOGEN PHOSPHORYLASE B / E.C.2.4.1.1


Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLESkeletal muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Sugar ChemComp-D6G / 2-deoxy-6-O-phosphono-alpha-D-glucopyranose / 2-deoxy-6-O-phosphono-alpha-D-arabino-hexopyranose / 2-deoxy-alpha-D-glucopyranose 6-phosphate / 2-deoxy-6-O-phosphono-alpha-D-glucose / 2-deoxy-6-O-phosphono-D-glucose / 2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 244.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O8P
IdentifierTypeProgram
a-D-2-deoxy-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.47 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: THE PROTEIN WAS CRYSTALLISED FROM 10 MM BES, PH 6.7, 3 MM DITHIOTHREITOL, 0.1 MM EDTA, 0.02% SODIUM AZIDE. THE CRYSTALS WERE THEN SOAKED FOR ONE HOUR IN 100 MM 2-DEOXY-D-GLUCOSE-6-PHOSPHATE. ...Details: THE PROTEIN WAS CRYSTALLISED FROM 10 MM BES, PH 6.7, 3 MM DITHIOTHREITOL, 0.1 MM EDTA, 0.02% SODIUM AZIDE. THE CRYSTALS WERE THEN SOAKED FOR ONE HOUR IN 100 MM 2-DEOXY-D-GLUCOSE-6-PHOSPHATE., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1DITHIOTHREITOL11
2BES11
3EDTAEthylenediaminetetraacetic acid11
4NAN311
Crystal grow
*PLUS
Details: Oikonomakos, N.G., (1985) Biochim. Biophys. Acta, 832, 248.
Components of the solutions
*PLUS
IDCrystal-ID
11
21
31
41

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Date: Aug 26, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→28.17 Å / Num. obs: 41448 / % possible obs: 94.7 % / Redundancy: 1.82 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 12
Reflection shellResolution: 2.3→2.4 Å / % possible all: 76.8
Reflection
*PLUS
Num. measured all: 75440

-
Processing

Software
NameVersionClassification
X-PLOR3.851refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PRJ

2prj


Resolution: 2.3→28.17 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 --RANDOM
Rwork0.192 ---
obs0.192 41448 94.7 %-
all-41448 --
Refinement stepCycle: LAST / Resolution: 2.3→28.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6749 0 30 255 7034
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.75
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 40308 / σ(F): 0 / Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg3.1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.75

+
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