[English] 日本語
Yorodumi
- PDB-2f3p: Crystal Structure of the glycogen phosphorylase B / N-(beta-D-glu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2f3p
TitleCrystal Structure of the glycogen phosphorylase B / N-(beta-D-glucopyranosyl)oxamic acid complex
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / glycogenolysis / type 2 diabetes
Function / homology
Function and homology information


glycogen phosphorylase / glycogen 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
N-(carboxycarbonyl)-beta-D-glucopyranosylamine / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.94 Å
AuthorsOikonomakos, N.G. / Leonidas, D.D.
CitationJournal: Bioorg.Med.Chem. / Year: 2006
Title: Binding of oxalyl derivatives of beta-d-glucopyranosylamine to muscle glycogen phosphorylase b.
Authors: Hadjiloi, T. / Tiraidis, C. / Chrysina, E.D. / Leonidas, D.D. / Oikonomakos, N.G. / Tsipos, P. / Gimisis, T.
History
DepositionNov 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / 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 1.5Aug 23, 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, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7903
Polymers97,2911
Non-polymers4982
Water6,323351
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,5796
Polymers194,5822
Non-polymers9974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6640 Å2
ΔGint-10 kcal/mol
Surface area55990 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)127.977, 127.977, 115.697
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsDimeric glycogen phosphorylase is the physiologiacally active species

-
Components

#1: Protein Glycogen phosphorylase, muscle form / Myophosphorylase


Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Strain: Rabbit / Tissue: Muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Sugar ChemComp-4GP / N-(carboxycarbonyl)-beta-D-glucopyranosylamine / N-(BETA-D-GLUCOPYRANOSYL)OXAMIC ACID / N-(carboxycarbonyl)-beta-D-glucosylamine / N-(carboxycarbonyl)-D-glucosylamine / N-(carboxycarbonyl)-glucosylamine


Type: D-saccharide / Mass: 251.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13NO8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7
Details: 10 mM Bes buffer, 3 mM DDT, pH 6.7, SMALL TUBES, temperature 289K

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.86 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2004
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.86 Å / Relative weight: 1
ReflectionResolution: 1.94→30 Å / Num. all: 71101 / Num. obs: 71101 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 22.6 Å2 / Rsym value: 0.055 / Net I/σ(I): 10.7
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 3500 / Rsym value: 0.415 / % possible all: 99.5

-
Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2PRJ

2prj


Resolution: 1.94→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2164 3608 RANDOM
Rwork0.1926 --
all0.193 71076 -
obs0.193 71076 -
Displacement parametersBiso mean: 29.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.237 Å20 Å20 Å2
2---3.237 Å20 Å2
3---6.473 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.94→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6589 0 32 351 6972
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006071
X-RAY DIFFRACTIONc_angle_deg1.26378
X-RAY DIFFRACTIONc_dihedral_angle_d21.92322
X-RAY DIFFRACTIONc_improper_angle_d0.82913
LS refinement shellResolution: 1.94→1.97 Å
RfactorNum. reflection% reflection
Rfree0.2981 345 -
Rwork0.2381 --
obs-6604 94.2 %

+
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