[English] 日本語
Yorodumi
- PDB-1vpe: CRYSTALLOGRAPHIC ANALYSIS OF PHOSPHOGLYCERATE KINASE FROM THE HYP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vpe
TitleCRYSTALLOGRAPHIC ANALYSIS OF PHOSPHOGLYCERATE KINASE FROM THE HYPERTHERMOPHILIC BACTERIUM THERMOTOGA MARITIMA
ComponentsPHOSPHOGLYCERATE KINASE
KeywordsTRANSFERASE / PHOSPHOGLYCERATE KINASE / THERMOTOGA MARITIMA / HYPERTHERMOSTABILITY / CRYSTAL / AMP-PNP / 3-PGA
Function / homology
Function and homology information


phosphoglycerate kinase / phosphoglycerate kinase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / ADP binding / fatty acid biosynthetic process / phosphorylation / ATP binding / 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. / Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. ...Phosphoglycerate kinase, N-terminal domain / Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase-type TIM barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-PHOSPHOGLYCERIC ACID / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Bifunctional PGK/TIM
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsAuerbach, G. / Huber, R. / Graettinger, M. / Zaiss, K. / Schurig, H. / Jaenicke, R. / Jacob, U.
Citation
Journal: Structure / Year: 1997
Title: Closed structure of phosphoglycerate kinase from Thermotoga maritima reveals the catalytic mechanism and determinants of thermal stability.
Authors: Auerbach, G. / Huber, R. / Grattinger, M. / Zaiss, K. / Schurig, H. / Jaenicke, R. / Jacob, U.
#1: Journal: Biol.Chem. / Year: 1997
Title: Crystallographic Analysis of Phosphoglycerate Kinase from the Hyperthermophilic Bacterium Thermotoga Maritima
Authors: Auerbach, G. / Jacob, U. / Grattinger, M. / Schurig, H. / Jaenicke, R.
History
DepositionMay 6, 1997Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / software / 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_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7624
Polymers43,0461
Non-polymers7173
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.009, 76.864, 87.501
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein PHOSPHOGLYCERATE KINASE


Mass: 43045.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Cellular location (production host): CYTOSOL / Production host: Escherichia coli (E. coli) / References: UniProt: P36204, 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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


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


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growDetails: PEG 3000/8000
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117 mg/mlprotein1drop
25 mMMops1drop
32 mMAMP-PNP1drop
42 mM3-phosphoglycerate1drop
52 mM1dropMgCl2
65 %PEG30001reservoir
720 %PEG80001reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→8 Å / Num. obs: 27144 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.07
Reflection shellHighest resolution: 2 Å / % possible all: 74.3
Reflection
*PLUS
Num. measured all: 106055
Reflection shell
*PLUS
% possible obs: 74.3 %

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMV. 5.23data reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2→8 Å / Rfactor Rfree: 0.288 / Rfactor Rwork: 0.198 / Rfactor obs: 0.198 / Cross valid method: R-FREE / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3026 0 0 249 3275
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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