[English] 日本語
Yorodumi
- PDB-1e2o: CATALYTIC DOMAIN FROM DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1e2o
TitleCATALYTIC DOMAIN FROM DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE
ComponentsDIHYDROLIPOAMIDE SUCCINYLTRANSFERASE
KeywordsTRANSFERASE / ACYLTRANSFERASE / KETOGLUTARATE DEHYDROGENASE MULTIENZYME COMPLEX
Function / homologyDihydrolipoamide succinyltransferase / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Peripheral subunit-binding (PSBD) domain profile. / Biotinyl/lipoyl domain profile. / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / e3 binding domain / Biotin/lipoyl attachment / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxo acid dehydrogenase, lipoyl-binding site / Peripheral subunit-binding domain ...Dihydrolipoamide succinyltransferase / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Peripheral subunit-binding (PSBD) domain profile. / Biotinyl/lipoyl domain profile. / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / e3 binding domain / Biotin/lipoyl attachment / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxo acid dehydrogenase, lipoyl-binding site / Peripheral subunit-binding domain / Biotin-requiring enzyme / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily / E3-binding domain superfamily / oxoglutarate dehydrogenase complex / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / L-lysine catabolic process to acetyl-CoA via saccharopine / lipoic acid binding / tricarboxylic acid cycle / cytosol / Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex / Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 3 Å resolution
AuthorsKnapp, J.E. / Mitchell, D.T. / Yazdi, M.A. / Ernst, S.R. / Reed, L.J. / Hackert, M.L.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of the truncated cubic core component of the Escherichia coli 2-oxoglutarate dehydrogenase multienzyme complex.
Authors: Knapp, J.E. / Mitchell, D.T. / Yazdi, M.A. / Ernst, S.R. / Reed, L.J. / Hackert, M.L.
#1: Journal: Science / Year: 1992
Title: Atomic Structure of the Cubic Core of the Pyruvate Dehydrogenase Multienzyme Complex
Authors: Mattevi, A. / Obmolova, G. / Schulze, E. / Kalk, K.H. / Westphal, A.H. / De Kok, A. / Hol, W.G.
#2: Journal: Eur.J.Biochem. / Year: 1984
Title: Nucleotide Sequence of the Sucb Gene Encoding the Dihydrolipoamide Succinyltransferase of Escherichia Coli K12 and Homology with the Corresponding Acetyltransferase
Authors: Spencer, M.E. / Darlison, M.G. / Stephens, P.E. / Duckenfield, I.K. / Guest, J.R.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1971
Title: Crystallization and Preliminary Structural Analysis of Dihydrolipoyl Transsuccinylase, the Core of the 2-Oxoglutarate Dehydrogenase Complex
Authors: Derosier, D.J. / Oliver, R.M. / Reed, L.J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 26, 1998 / Release: Dec 2, 1998
RevisionDateData content typeGroupProviderType
1.0Dec 2, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2032
Polyers26,1071
Non-polymers961
Water28816
1
A: DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)628,88448
Polyers626,57824
Non-polymers2,30624
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area (Å2)86500
ΔGint (kcal/M)-561
Surface area (Å2)219200
MethodPISA,PQS
Unit cell
γ
α
β
Length a, b, c (Å)222.800, 222.800, 222.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF 4 3 2

-
Components

#1: Protein/peptide DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE / E2O


Mass: 26107.420 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 172 - 404 / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Gene: SUCB / Plasmid name: PGEX-2T / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / Strain (production host): JM101
References: UniProt: P07016, UniProt: P0AFG6*PLUS, dihydrolipoyllysine-residue succinyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Formula: SO4 / Sulfate
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Formula: H2O / Water

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.4 / Density percent sol: 72 %
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 1.2M AMMONIUM SULFATE, 1% ETHANOL, 50 MM POTASSIUM PHOSPHATE, PH 7.0
Crystal grow
*PLUS
pH: 7.3 / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
120 mg/mlprotein1drop
250 mMpotassium phosphate1drop
31 mMdithiothreitol1drop
41 mMEDTA1drop
51 mMbenzamidine1drop
61.2 Mammonium sulfate1reservoir
71 %(v/v)ethanol1reservoir

-
Data collection

DiffractionMean temperature: 298 kelvins
SourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Details: MIRRORS / Detector: IMAGE PLATE / Collection date: Mar 1, 1994
RadiationMonochromator: SI(111) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionD resolution high: 3 Å / D resolution low: 2 Å / Number obs: 9906 / Observed criterion sigma I: 3 / Rsym value: 0.046 / NetI over sigmaI: 13 / Redundancy: 4.1 % / Percent possible obs: 98.5
Reflection shellHighest resolution: 3 Å / Lowest resolution: 3.16 Å / MeanI over sigI obs: 4.9 / Rsym value: 0.145 / Redundancy: 4.5 % / Percent possible all: 1
Reflection
*PLUS
Rmerge I obs: 0.046
Reflection shell
*PLUS
Percent possible obs: 1 / Rmerge I obs: 0.145

-
Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(ROTAVATAdata scaling
AGROVATA)data scaling
X-PLOR3.851phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EAA
Details: BULK SOLVENT MODEL AND RESOLUTION-DEPENDENT WEIGHTING SCHEME USED.
R Free selection details: RANDOM / Data cutoff high absF: 1 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / Sigma F: 0
Displacement parametersB iso mean: 33.6 Å2 / Aniso B11: 0 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 0 Å2 / Aniso B23: 0 Å2 / Aniso B33: 0 Å2
Least-squares processR factor R free: 0.249 / R factor R free error: 0.008 / R factor R work: 0.205 / R factor obs: 0.205 / Highest resolution: 3 Å / Lowest resolution: 2 Å / Number reflection R free: 1001 / Number reflection obs: 9696 / Percent reflection R free: 10.3 / Percent reflection obs: 97.4
Refine analyzeLuzzati coordinate error free: 0.37 Å / Luzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.51 Å / Luzzati sigma a obs: 0.4 Å
Refine hist #LASTHighest resolution: 3 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 1726 / Nucleic acid: 0 / Ligand: 5 / Solvent: 16 / Total: 1747
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.010
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.37
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
Refine LS shellHighest resolution: 3 Å / R factor R free: 0.341 / R factor R free error: 0.028 / R factor R work: 0.261 / Lowest resolution: 3.19 Å / Number reflection R free: 145 / Number reflection R work: 1397 / Total number of bins used: 6 / Percent reflection R free: 9.4 / Percent reflection obs: 96.1
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3SO4.PARSO4.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.37

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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