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- PDB-1cqj: CRYSTAL STRUCTURE OF DEPHOSPHORYLATED E. COLI SUCCINYL-COA SYNTHETASE -

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Basic information

Entry
Database: PDB / ID: 1cqj
TitleCRYSTAL STRUCTURE OF DEPHOSPHORYLATED E. COLI SUCCINYL-COA SYNTHETASE
Components
  • SUCCINYL-COA SYNTHETASE ALPHA CHAIN
  • SUCCINYL-COA SYNTHETASE BETA CHAIN
KeywordsLIGASE / ATP-GRASP FOLD / ROSSMANN FOLD
Function / homology
Function and homology information


succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / tricarboxylic acid cycle / nucleotide binding / magnesium ion binding / ATP binding ...succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / tricarboxylic acid cycle / nucleotide binding / magnesium ion binding / ATP binding / cytoplasm / cytosol
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, subdomain 1 / ATP-grasp fold, B domain / 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 / PHOSPHATE ION / Succinate--CoA ligase [ADP-forming] subunit alpha / Succinate--CoA ligase [ADP-forming] subunit beta / 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 / SYNCHROTRON / Resolution: 2.9 Å
AuthorsJoyce, M.A. / Fraser, M.E. / James, M.N.G. / Bridger, W.A. / Wolodko, W.T.
Citation
Journal: Biochemistry / Year: 2000
Title: ADP-binding site of Escherichia coli succinyl-CoA synthetase revealed by x-ray crystallography.
Authors: Joyce, M.A. / Fraser, M.E. / James, M.N. / Bridger, W.A. / Wolodko, W.T.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: A Detailed Structural Description of Escherichia Coli Succinyl-CoA Synthetase
Authors: Fraser, M.E. / James, M.N.G. / Bridger, W.A. / Wolodko, W.T.
#2: Journal: J.Biol.Chem. / Year: 1994
Title: The crystal structure of succinyl-CoA synthetase from Escherichia coli at 2.5A resolution
Authors: Wolodko, W.T. / Fraser, M.E. / James, M.N.G. / Bridger, W.A.
#3: 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
DepositionAug 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)143,80311
Polymers141,1204
Non-polymers2,6827
Water5,945330
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.820, 98.820, 404.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Cell settingtetragonal
Space group name H-MP4322
DetailsHeterotetramer formed by two alpha beta-dimers related by a crystallographic two-fold axis.

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Components

#1: Protein SUCCINYL-COA SYNTHETASE ALPHA CHAIN / E.C.6.2.1.5 / SCS-ALPHA


Mass: 29436.902 Da / Num. of mol.: 2 / Fragment: ALPHA SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P07459, UniProt: P0AGE9*PLUS, succinate-CoA ligase (ADP-forming)
#2: Protein SUCCINYL-COA SYNTHETASE BETA CHAIN / E.C.6.2.1.5 / SCS-BETA


Mass: 41123.152 Da / Num. of mol.: 2 / Fragment: BETA SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P07460, UniProt: P0A836*PLUS, succinate-CoA ligase (ADP-forming)
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.85 %
Crystal growTemperature: 294 K / Method: microdialysis / pH: 7.3
Details: ammonium sulfate, potassium phosphate, coenzyme A, pH 7.3, MICRODIALYSIS, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.9 Mammonium sulfate11
20.1 Mpotassium phosphate11
31 mMdithiothreitol11
40.1 mMCoA11
50.1 mMEDTA11

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 4, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 45002 / Num. obs: 45002 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.092
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.35 / Num. unique all: 6283 / % possible all: 96.6
Reflection
*PLUS
% possible obs: 98.7 % / Num. measured all: 258739
Reflection shell
*PLUS
Lowest resolution: 3.08 Å / Num. measured obs: 19746

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Processing

Software
NameVersionClassification
BIOMOLPACKAGEmodel building
CNSrefinement
WEISdata reduction
SCALKB2data scaling
KBAPLYdata scaling
RefinementResolution: 2.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Maximum likelihood refinement in CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 5121 11.4 %random
Rwork0.172 ---
all0.178 45002 --
obs0.178 45002 98.6 %-
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9892 0 133 330 10355
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.9
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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