[English] 日本語
Yorodumi
- PDB-2g67: E. Coli Pyruvate Dehydrogenase E1 Component (Apoenzyme) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2g67
TitleE. Coli Pyruvate Dehydrogenase E1 Component (Apoenzyme)
ComponentsPyruvate dehydrogenase E1 component
KeywordsOXIDOREDUCTASE / PYRUVATE DEHYDROGENASE E1 COMPONENT / APOENZYME / HOMODIMER
Function / homology
Function and homology information


: / pyruvate dehydrogenase activity / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / pyruvate catabolic process / pyruvate dehydrogenase complex / thiamine pyrophosphate binding / small molecule binding / glycolytic process / molecular adaptor activity ...: / pyruvate dehydrogenase activity / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / pyruvate catabolic process / pyruvate dehydrogenase complex / thiamine pyrophosphate binding / small molecule binding / glycolytic process / molecular adaptor activity / magnesium ion binding / protein homodimerization activity / membrane / identical protein binding / cytosol
Similarity search - Function
Pyruvate dehydrogenase E1 component, N-terminal / Pyruvate dehydrogenase E1 component, middle domain / Pyruvate dehydrogenase E1 component middle domain / Pyruvate dehydrogenase E1 component / Transketolase, thiamine diphosphate binding domain / Transketolase, N-terminal / Rossmann fold - #920 / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold ...Pyruvate dehydrogenase E1 component, N-terminal / Pyruvate dehydrogenase E1 component, middle domain / Pyruvate dehydrogenase E1 component middle domain / Pyruvate dehydrogenase E1 component / Transketolase, thiamine diphosphate binding domain / Transketolase, N-terminal / Rossmann fold - #920 / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Pyruvate dehydrogenase E1 component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.32 Å
AuthorsFurey, W. / Chandrasekhar, K. / Arjunan, P.
CitationJournal: ACTA CRYSTALLOGR.,SECT.D / Year: 2006
Title: Active-site changes in the pyruvate dehydrogenase multienzyme complex E1 apoenzyme component from Escherichia coli observed at 2.32 A resolution.
Authors: Chandrasekhar, K. / Arjunan, P. / Sax, M. / Nemeria, N. / Jordan, F. / Furey, W.
History
DepositionFeb 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyruvate dehydrogenase E1 component
B: Pyruvate dehydrogenase E1 component


Theoretical massNumber of molelcules
Total (without water)199,3142
Polymers199,3142
Non-polymers00
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11390 Å2
ΔGint-41 kcal/mol
Surface area50530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.610, 140.630, 81.910
Angle α, β, γ (deg.)90.00, 102.87, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 463 / 2: CIS PROLINE - PRO B 463

-
Components

#1: Protein Pyruvate dehydrogenase E1 component


Mass: 99657.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aceE / Plasmid: JRG PGS878 / Production host: Escherichia coli (E. coli) / Strain (production host): JRG 3456
References: UniProt: P0AFG8, pyruvate dehydrogenase (acetyl-transferring)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG2000 MONOMETHYL ETHER, 2-PROPANOL, SODIUM AZIDE, HEPES BUFFER, PH 7.00, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Feb 23, 2001 / Details: OSMIC MIRRORS
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.31→34.62 Å / Num. all: 71391 / Num. obs: 71362 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.85 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.01
Reflection shellResolution: 2.31→2.4 Å / Mean I/σ(I) obs: 6.6 / % possible all: 44.1

-
Processing

Software
NameVersionClassification
X-GENdata scaling
FBSCALEdata reduction
PHASESphasing
CNS1.1refinement
X-GENdata reduction
FBSCALEdata scaling
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: 1L8A

1l8a


Resolution: 2.32→34.62 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 157974.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 3588 5.1 %RANDOM
Rwork0.212 ---
all0.234 70895 --
obs0.212 70893 91.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.946 Å2 / ksol: 0.362334 e/Å3
Displacement parametersBiso mean: 15.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-1.99 Å2
2---0.86 Å20 Å2
3---1.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 2.32→34.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12702 0 0 448 13150
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.546
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it3.0411.5
X-RAY DIFFRACTIONc_mcangle_it3.9452
X-RAY DIFFRACTIONc_scbond_it4.772
X-RAY DIFFRACTIONc_scangle_it5.3012.5
LS refinement shellResolution: 2.32→2.4 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.304 208 5.4 %
Rwork0.203 3641 -
obs--49.8 %

+
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