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- PDB-2cts: CRYSTALLOGRAPHIC REFINEMENT AND ATOMIC MODELS OF TWO DIFFERENT FO... -

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Basic information

Entry
Database: PDB / ID: 2cts
TitleCRYSTALLOGRAPHIC REFINEMENT AND ATOMIC MODELS OF TWO DIFFERENT FORMS OF CITRATE SYNTHASE AT 2.7 AND 1.7 ANGSTROMS RESOLUTION
ComponentsCITRATE SYNTHASE
KeywordsOXO-ACID-LYASE
Function / homology
Function and homology information


Maturation of TCA enzymes and regulation of TCA cycle / citrate (Si)-synthase / citrate synthase activity / Citric acid cycle (TCA cycle) / : / citrate metabolic process / Mitochondrial protein degradation / tricarboxylic acid cycle / carbohydrate metabolic process / mitochondrial matrix / identical protein binding
Similarity search - Function
Citrate synthase, eukaryotic-type / Citrate Synthase; domain 1 / Citrate Synthase, domain 1 / Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain ...Citrate synthase, eukaryotic-type / Citrate Synthase; domain 1 / Citrate Synthase, domain 1 / Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / COENZYME A / Citrate synthase, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsRemington, S. / Wiegand, G. / Huber, R.
Citation
Journal: J.Mol.Biol. / Year: 1982
Title: Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1.7 A resolution.
Authors: Remington, S. / Wiegand, G. / Huber, R.
#1: Journal: Eur.J.Biochem. / Year: 1979
Title: Crystal Structure Analysis of the Tetragonal Crystal Form and Preliminary Molecular Model of Pig-Heart Citrate Synthase
Authors: Wiegand, G. / Kukla, D. / Scholze, H. / Jones, T.A. / Huber, R.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1981
Title: Primary Structure of Porcine Heart Citrate Synthase
Authors: Bloxham, D.P. / Parmelee, D.C. / Kumar, S. / Wade, R.D. / Ericsson, L.H. / Neurath, H. / Walsh, K.A. / Titani, K.
History
DepositionJan 27, 1984Processing site: BNL
Revision 1.0Jul 20, 1984Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: CITRATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9093
Polymers48,9491
Non-polymers9602
Water1,71195
1
A: CITRATE SYNTHASE
hetero molecules

A: CITRATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,8176
Polymers97,8982
Non-polymers1,9194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13380 Å2
ΔGint-41 kcal/mol
Surface area30140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.140, 78.250, 58.400
Angle α, β, γ (deg.)90.00, 78.50, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: AN OCCUPANCY OF 0.0 INDICATES THAT THE ATOM COULD NOT BE FOUND IN THE ELECTRON DENSITY MAP AND IS INCLUDED AS A DUMMY ATOM.

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Components

#1: Protein CITRATE SYNTHASE


Mass: 48949.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00889, EC: 4.1.3.7
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal grow
*PLUS
pH: 5.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.0 mg/mlprotein1drop
20.8 Mcitrate1drop
30.9-1.0 Msodium citrate1reservoir

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Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 2→5 Å / Rfactor Rwork: 0.161
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 61 95 3598
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.014
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.6
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 5 Å / Rfactor obs: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_angle_d / Dev ideal: 2.6

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