[English] 日本語
Yorodumi
- PDB-4n72: Catalytic domain from dihydrolipoamide acetyltransferase of pyruv... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n72
TitleCatalytic domain from dihydrolipoamide acetyltransferase of pyruvate dehydrogenase from Escherichia coli
ComponentsPyruvate dehydrogenase (Dihydrolipoyltransacetylase component)
KeywordsTRANSFERASE / dihydrolipoamide acetyltransferase catalytic domain / pyruvate dehydrogenase / acetyltransferase
Function / homology
Function and homology information


dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / pyruvate dehydrogenase complex / glycolytic process
Similarity search - Function
Dihydrolipoamide acetyltransferase pyruvate dehydrogenase complex / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain ...Dihydrolipoamide acetyltransferase pyruvate dehydrogenase complex / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetyltransferase component of pyruvate dehydrogenase complex
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsChandrasekhar, K. / Arjunan, P. / Furey, W.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure and Function of the Catalytic Domain of the Dihydrolipoyl Acetyltransferase Component in Escherichia coli Pyruvate Dehydrogenase Complex.
Authors: Wang, J. / Nemeria, N.S. / Chandrasekhar, K. / Kumaran, S. / Arjunan, P. / Reynolds, S. / Calero, G. / Brukh, R. / Kakalis, L. / Furey, W. / Jordan, F.
History
DepositionOct 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Sep 20, 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 (Dihydrolipoyltransacetylase component)
B: Pyruvate dehydrogenase (Dihydrolipoyltransacetylase component)
C: Pyruvate dehydrogenase (Dihydrolipoyltransacetylase component)


Theoretical massNumber of molelcules
Total (without water)82,4733
Polymers82,4733
Non-polymers00
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12430 Å2
ΔGint-95 kcal/mol
Surface area32120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.560, 92.830, 110.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Pyruvate dehydrogenase (Dihydrolipoyltransacetylase component) / Pyruvate dehydrogenase dihydrolipoyltransacetylase component


Mass: 27491.049 Da / Num. of mol.: 3 / Fragment: E2 Catalytic Domain (UNP residues 382-630)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aceF, ECs0119, Z0125 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8X966, dihydrolipoyllysine-residue acetyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 49.02 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 7
Details: 20% PEG 3350, 0.2M sodium thiocyanate, pH 7.00, VAPOR DIFFUSION, temperature 296.0K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 7, 2011 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.25→21.4 Å / Num. all: 38565 / Num. obs: 38560 / % possible obs: 99.9 % / Observed criterion σ(F): 0.01 / Observed criterion σ(I): 0 / Redundancy: 6.04 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 3.7
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 5.77 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 1.8 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DPC

1dpc


Resolution: 2.25→21.398 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 30.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1885 4.99 %random
Rwork0.208 ---
all0.216 38565 --
obs0.21 37763 98.08 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.934 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.0091 Å20 Å20 Å2
2---1.9877 Å20 Å2
3----3.0214 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å / Luzzati d res low obs: 21.4 Å
Refinement stepCycle: LAST / Resolution: 2.25→21.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5725 0 0 318 6043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035830
X-RAY DIFFRACTIONf_angle_d0.6977869
X-RAY DIFFRACTIONf_dihedral_angle_d12.1142210
X-RAY DIFFRACTIONf_chiral_restr0.048908
X-RAY DIFFRACTIONf_plane_restr0.0051005
LS refinement shellResolution: 2.25→2.31 Å
RfactorNum. reflection% reflection
Rfree0.366 150 -
Rwork0.354 --
obs-2596 99 %

+
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