[English] 日本語
Yorodumi
- PDB-1qpg: 3-PHOSPHOGLYCERATE KINASE, MUTATION R65Q -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qpg
Title3-PHOSPHOGLYCERATE KINASE, MUTATION R65Q
Components3-PHOSPHOGLYCERATE KINASE
KeywordsPHOSPHOTRANSFERASE (CARBOXYL ACCEPTOR) / KINASE / ACETYLATION / GLYCOLYSIS
Function / homology
Function and homology information


Gluconeogenesis / Glycolysis / phosphoglycerate kinase / phosphoglycerate kinase activity / gluconeogenesis / glycolytic process / ADP binding / calmodulin binding / phosphorylation / mitochondrion ...Gluconeogenesis / Glycolysis / phosphoglycerate kinase / phosphoglycerate kinase activity / gluconeogenesis / glycolytic process / ADP binding / calmodulin binding / phosphorylation / mitochondrion / ATP 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 / MAGNESIUM-5'-ADENYLY-IMIDO-TRIPHOSPHATE / Phosphoglycerate kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsMcphillips, T.M. / Hsu, B.T. / Sherman, M.A. / Mas, M.T. / Rees, D.C.
Citation
Journal: Biochemistry / Year: 1996
Title: Structure of the R65Q mutant of yeast 3-phosphoglycerate kinase complexed with Mg-AMP-PNP and 3-phospho-D-glycerate.
Authors: McPhillips, T.M. / Hsu, B.T. / Sherman, M.A. / Mas, M.T. / Rees, D.C.
#1: Journal: Protein Sci. / Year: 1992
Title: Characterization of the Structure and Properties of the His 62-->Ala and Arg 38-->Ala Mutants of Yeast Phosphoglycerate Kinase: An Investigation of the Catalytic and Activatory Sites by Site- ...Title: Characterization of the Structure and Properties of the His 62-->Ala and Arg 38-->Ala Mutants of Yeast Phosphoglycerate Kinase: An Investigation of the Catalytic and Activatory Sites by Site-Directed Mutagenesis and NMR
Authors: Sherman, M.A. / Fairbrother, W.J. / Mas, M.T.
#2: Journal: Protein Eng. / Year: 1991
Title: Site-Directed Mutations of Arginine 65 at the Periphery of the Active Site Cleft of Yeast 3-Phosphoglycerate Kinase Enhance the Catalytic Activity and Eliminate Anion-Dependent Activation
Authors: Sherman, M.A. / Dean, S.A. / Mathiowetz, A.M. / Mas, M.T.
#3: Journal: J.Biol.Chem. / Year: 1990
Title: Probing the Role of Arginines and Histidines in the Catalytic Function and Activation of Yeast 3-Phosphoglycerate Kinase by Site-Directed Mutagenesis
Authors: Sherman, M.A. / Szpikowska, B.K. / Dean, S.A. / Mathiowetz, A.M. / Mcqueen, N.L. / Mas, M.T.
History
DepositionJan 4, 1996Processing site: BNL
Revision 1.0Jun 10, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Refinement description
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Category: computing
Revision 1.5Nov 3, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3573
Polymers44,6411
Non-polymers7162
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.000, 70.100, 82.300
Angle α, β, γ (deg.)90.00, 122.20, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein 3-PHOSPHOGLYCERATE KINASE / PGK


Mass: 44641.059 Da / Num. of mol.: 1 / Mutation: R65Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: YEP9T-PGK / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): PGK-XSB44-35D / References: UniProt: P00560, phosphoglycerate kinase
#2: Chemical ChemComp-MAP / MAGNESIUM-5'-ADENYLY-IMIDO-TRIPHOSPHATE


Mass: 529.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16MgN6O12P3
#3: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 mg/mlR65Q PGK1drop
210 mM5'-adenylylimidodiphosphate1drop
410 mMD-(-)-3-phosphoglycerate1drop
621 %PEG80001reservoir
720 mMmagnesium acetate1reservoir
80.02 %1reservoirNaN3
950 mMHEPES1reservoir
3tetralithium salt (AMP-PNP)1drop
5disodium salt (3-PG)1drop

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 30, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.43→40.7 Å / Num. obs: 16281 / % possible obs: 92.4 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.076
Reflection
*PLUS
Num. measured all: 100828

-
Processing

Software
NameVersionClassification
X-PLOR3.1refinement
TNTrefinement
X-PLOR3.1model building
XENGENdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.4→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.185 --
obs0.185 13387 78.3 %
Displacement parametersBiso mean: 33.9 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3146 0 43 82 3271
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.781
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.67
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.262
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 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.67
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.262

+
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://pdbjlvh1.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