[English] 日本語
Yorodumi
- PDB-3pgk: The structure of yeast phosphoglycerate kinase at 0.25 nm resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pgk
TitleThe structure of yeast phosphoglycerate kinase at 0.25 nm resolution
ComponentsPHOSPHOGLYCERATE KINASE
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE(CARBOXYL AS ACCEPTOR)
Function / homology
Function and homology information


Gluconeogenesis / Glycolysis / phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / gluconeogenesis / ADP binding / mitochondrion / ATP binding / metal ion binding ...Gluconeogenesis / Glycolysis / phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / gluconeogenesis / ADP binding / mitochondrion / ATP binding / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Phosphoglycerate kinase, N-terminal domain / Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-PHOSPHOGLYCERIC ACID / ADENOSINE-5'-TRIPHOSPHATE / Phosphoglycerate kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsShaw, P.J. / Walker, N.P. / Watson, H.C.
Citation
#1: Journal: Biochem.J. / Year: 1983
Title: The Complete Amino Acid Sequence of Yeast Phosphoglycerate Kinase
Authors: Perkins, R.E. / Conroy, S.C. / Dunbar, B. / Fothergill, L.A. / Tuite, M.F. / Dobson, M.J. / Kingsman, S.M. / Kingsman, A.J.
#2: Journal: Embo J. / Year: 1982
Title: Sequence and Structure of Yeast Phosphoglycerate Kinase
Authors: Watson, H.C. / Walker, N.P.C. / Shaw, P.J. / Bryant, T.N. / Wendell, P.L. / Fothergill, L.A. / Perkins, R.E. / Conroy, S.C. / Dobson, M.J. / Tuite, M.F. / Kingsman, A.J. / Kingsman, S.M.
#3: Journal: Nature / Year: 1974
Title: Structure of Yeast Phosphoglycerate Kinase
Authors: Bryant, T.N. / Watson, H.C. / Wendell, P.L.
#4: Journal: Nature New Biol. / Year: 1972
Title: Low Resolution Structure of Yeast Phosphoglycerate Kinase
Authors: Wendell, P.L. / Bryant, T.N. / Watson, H.C.
#5: Journal: J.Mol.Biol. / Year: 1971
Title: Crystallographic Study of Yeast Phosphoglycerate Kinase
Authors: Watson, H.C. / Wendell, P.L. / Scopes, R.K.
History
DepositionJul 15, 1982Processing site: BNL
SupersessionSep 24, 1982ID: 1PGK
Revision 1.0Sep 24, 1982Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details
Remark 700SHEET CAUTION. THE DEFINITION OF THE BEGINNING AND END OF HELICES AND SHEET STRANDS GIVEN BELOW ...SHEET CAUTION. THE DEFINITION OF THE BEGINNING AND END OF HELICES AND SHEET STRANDS GIVEN BELOW DEPENDS SOMEWHAT ON THE CRITERIA USED TO DEFINE A *GOOD* HYDROGEN BOND. TURNS LISTED BELOW ARE THOSE WHERE CA(1)-CA(4) IS LESS THAN 5.7 ANGSTROMS AND O(1)-N(4) IS LESS THAN 3.2 ANGSTROMS. FULL TURN DEFINITION MUST AWAIT FURTHER REFINEMENT.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3704
Polymers44,6521
Non-polymers7183
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.600, 54.400, 93.000
Angle α, β, γ (deg.)90.00, 134.40, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: THIS ATOM MAY BE MAGNESIUM OR MANGANESE.

-
Components

#1: Protein PHOSPHOGLYCERATE KINASE


Mass: 44652.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P00560, phosphoglycerate kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.97 %

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

RefinementHighest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3148 0 43 0 3191

+
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