[English] 日本語
Yorodumi
- PDB-1c4t: CATALYTIC DOMAIN FROM TRIMERIC DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1c4t
TitleCATALYTIC DOMAIN FROM TRIMERIC DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE
ComponentsPROTEIN (DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE)
KeywordsTRANSFERASE / ACYLTRANSFERASE / KETOGLUTARATE DEHYDROGENASE MULTIENZYME COMPLEX
Function / homology
Function and homology information


L-lysine catabolic process to acetyl-CoA via saccharopine / oxoglutarate dehydrogenase complex / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / lipoic acid binding / tricarboxylic acid cycle / cytosol / cytoplasm
Similarity search - Function
Dihydrolipoamide succinyltransferase / 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 succinyltransferase / 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
Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex / Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKnapp, J.E. / Carroll, D. / Lawson, J.E. / Ernst, S.R. / Reed, L.J. / Hackert, M.L.
Citation
Journal: Protein Sci. / Year: 2000
Title: Expression, purification, and structural analysis of the trimeric form of the catalytic domain of the Escherichia coli dihydrolipoamide succinyltransferase.
Authors: Knapp, J.E. / Carroll, D. / Lawson, J.E. / Ernst, S.R. / Reed, L.J. / Hackert, M.L.
#1: 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.
#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.
History
DepositionSep 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE)
B: PROTEIN (DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE)
C: PROTEIN (DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8999
Polymers78,3223
Non-polymers5766
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9310 Å2
ΔGint-137 kcal/mol
Surface area28140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.175, 112.175, 134.417
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.674415, 0.682089, 0.2827), (0.04097, -0.41686, 0.908047), (0.737215, -0.600818, -0.309082)-56.812, 190.429, -1.071
2given(0.69522, 0.015427, 0.718632), (0.670704, -0.373478, -0.640836), (0.258507, 0.927511, -0.269996)-88.189, 76.587, 157.257

-
Components

#1: Protein PROTEIN (DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE) / E2O


Mass: 26107.420 Da / Num. of mol.: 3 / Fragment: CATALYTIC DOMAIN, RESIDUES 172 - 404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21(DE3) / Cellular location: MITOCHONDRIAMitochondrion / Gene: SUCB / Plasmid: PET-21A(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P07016, UniProt: P0AFG6*PLUS, dihydrolipoyllysine-residue succinyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
2100 mMHEPES1drop
31 Msodium acetate1reservoir
450 mMcadmium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 1, 1996 / Details: MSC MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→10 Å / Num. obs: 18669 / % possible obs: 95.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 57.3 Å2 / Rsym value: 10.3 / Net I/σ(I): 13.8
Reflection shellResolution: 3→3.1 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.6 / Rsym value: 30.9 / % possible all: 93.5
Reflection
*PLUS
Num. obs: 18677 / % possible obs: 95.8 % / Rmerge(I) obs: 0.103
Reflection shell
*PLUS
% possible obs: 93.5 % / Num. unique obs: 1798 / Rmerge(I) obs: 0.309

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E2O

1e2o


Resolution: 3→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1832 9.8 %RANDOM
Rwork0.257 ---
obs0.257 18669 95.9 %-
Displacement parametersBiso mean: 49.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4986 0 30 28 5044
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.23
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it12.771.5
X-RAY DIFFRACTIONx_mcangle_it16.552
X-RAY DIFFRACTIONx_scbond_it02
X-RAY DIFFRACTIONx_scangle_it02.5
LS refinement shellResolution: 3→3.18 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.399 283 9.5 %
Rwork0.339 2708 -
obs--93.3 %
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_deg25.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.23

+
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