[English] 日本語
Yorodumi
- PDB-1scu: THE CRYSTAL STRUCTURE OF SUCCINYL-COA SYNTHETASE FROM ESCHERICHIA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1scu
TitleTHE CRYSTAL STRUCTURE OF SUCCINYL-COA SYNTHETASE FROM ESCHERICHIA COLI AT 2.5 ANGSTROMS RESOLUTION
Components
  • SUCCINYL-COA SYNTHETASE, ALPHA SUBUNITSuccinyl coenzyme A synthetase
  • SUCCINYL-COA SYNTHETASE, BETA SUBUNITSuccinyl coenzyme A synthetase
KeywordsLIGASE (ATP-BINDING)
Function / homology
Function and homology information


succinate-CoA ligase complex / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (GDP-forming) activity / succinyl-CoA metabolic process / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / tricarboxylic acid cycle / nucleotide binding / magnesium ion binding / ATP binding ...succinate-CoA ligase complex / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (GDP-forming) activity / succinyl-CoA metabolic process / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / tricarboxylic acid cycle / nucleotide binding / magnesium ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Succinyl-CoA ligase, alpha subunit / Succinate--CoA synthetase, beta subunit / ATP-grasp fold, succinyl-CoA synthetase-type / ATP-grasp domain / Succinyl-CoA synthetase domains / ATP-citrate lyase/succinyl-CoA ligase, active site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. / Succinyl-CoA synthetase, beta subunit, conserved site ...Succinyl-CoA ligase, alpha subunit / Succinate--CoA synthetase, beta subunit / ATP-grasp fold, succinyl-CoA synthetase-type / ATP-grasp domain / Succinyl-CoA synthetase domains / ATP-citrate lyase/succinyl-CoA ligase, active site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. / Succinyl-CoA synthetase, beta subunit, conserved site / ATP-citrate lyase / succinyl-CoA ligases family signature 3. / ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Succinate--CoA ligase [ADP-forming] subunit alpha / Succinate--CoA ligase [ADP-forming] subunit beta / Succinate--CoA ligase [ADP-forming] subunit alpha
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsWolodko, W.T. / Fraser, M.E. / James, M.N.G. / Bridger, W.A.
Citation
Journal: J.Biol.Chem. / Year: 1994
Title: The crystal structure of succinyl-CoA synthetase from Escherichia coli at 2.5-A resolution.
Authors: Wolodko, W.T. / Fraser, M.E. / James, M.N. / Bridger, W.A.
#1: Journal: J.Biol.Chem. / Year: 1984
Title: Crystallization of Succinyl-Coa Synthetase from Escherichia Coli
Authors: Wolodko, W.T. / James, M.N.G. / Bridger, W.A.
History
DepositionNov 18, 1993Processing site: BNL
Revision 1.0Apr 20, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_status / software / struct_conn
Item: _pdbx_database_status.process_site / _software.classification / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SUCCINYL-COA SYNTHETASE, ALPHA SUBUNIT
B: SUCCINYL-COA SYNTHETASE, BETA SUBUNIT
D: SUCCINYL-COA SYNTHETASE, ALPHA SUBUNIT
E: SUCCINYL-COA SYNTHETASE, BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,9286
Polymers142,3934
Non-polymers1,5352
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.470, 98.470, 400.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Atom site foot note1: CIS PROLINE - PRO A 121 / 2: CIS PROLINE - PRO B 42 / 3: CIS PROLINE - PRO B 200 / 4: CIS PROLINE - PRO D 121 / 5: CIS PROLINE - PRO E 42 / 6: CIS PROLINE - PRO E 200
7: RESIDUE 246 OF EACH ALPHA SUBUNIT IS A PHOSPHORYLATED HISTIDINE.

-
Components

#1: Protein SUCCINYL-COA SYNTHETASE, ALPHA SUBUNIT / Succinyl coenzyme A synthetase


Mass: 29758.213 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
References: UniProt: P07459, UniProt: P0AGE9*PLUS, succinate-CoA ligase (ADP-forming)
#2: Protein SUCCINYL-COA SYNTHETASE, BETA SUBUNIT / Succinyl coenzyme A synthetase


Mass: 41438.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
References: UniProt: P0A836, succinate-CoA ligase (ADP-forming)
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAMINO-TERMINAL ANALYSIS OF THE ALPHA SUBUNIT INDICATES THAT THE FIRST RESIDUE IS A SERINE (W. A. ...AMINO-TERMINAL ANALYSIS OF THE ALPHA SUBUNIT INDICATES THAT THE FIRST RESIDUE IS A SERINE (W. A. BRIDGE, ENZYMES, 3RD ED. 10, 581-606 (1974)). IN THE GENE SEQUENCING PAPER, BUCK, SPENCER AND GUEST STATE THAT "[THE ASSUMPTION IS] THAT THE INITIATING FORMYLMETHIONINE IS REMOVED POSTTRANSLATIONALLY FROM THE ALPHA BUT NOT FROM THE BETA SUBUNIT" (D. BUCK, M. E. SPENCER, AND J. R. GUEST, BIOCHEMISTRY 24, 6245-6252 (1985)).

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.93 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7.3 / Method: microdialysis / Details: Wolodko, W.T., (1984) J. Biol. Chem., 259, 5316.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlenzyme11
21.9 Mammonium sulfate12
30.1 Mpotassium phosphate12
41 mMdithiothreitol12
50.1 mMCoA12
60.1 mMEDTA12

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→100 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.216 -
obs0.216 67272
Refinement stepCycle: LAST / Resolution: 2.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9982 0 96 110 10188
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.022
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_deg3.25
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

+
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