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- PDB-4cts: CRYSTAL STRUCTURE ANALYSIS AND MOLECULAR MODEL OF A COMPLEX OF CI... -

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Basic information

Entry
Database: PDB / ID: 4cts
TitleCRYSTAL STRUCTURE ANALYSIS AND MOLECULAR MODEL OF A COMPLEX OF CITRATE SYNTHASE WITH OXALOACETATE AND S-ACETONYL-COENZYME A
ComponentsCITRATE SYNTHASE
KeywordsOXO-ACID-LYASE
Function / homology
Function and homology information


Maturation of TCA enzymes and regulation of TCA cycle / citrate (Si)-synthase / Citric acid cycle (TCA cycle) / citrate synthase activity / : / 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
OXALOACETATE ION / Citrate synthase, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsRemington, S. / Wiegand, G. / Huber, R.
Citation
Journal: J.Mol.Biol. / Year: 1984
Title: Crystal structure analysis and molecular model of a complex of citrate synthase with oxaloacetate and S-acetonyl-coenzyme A
Authors: Wiegand, G. / Remington, S. / Deisenhofer, J. / Huber, R.
#1: 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 Angstroms Resolution
Authors: Remington, S. / Wiegand, G. / Huber, R.
#2: 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.
#3: 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 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 28, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CITRATE SYNTHASE
B: CITRATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2164
Polymers97,9542
Non-polymers2622
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10130 Å2
ΔGint-52 kcal/mol
Surface area31570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.540, 101.540, 224.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
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.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.95607, -0.29312, 0.00217), (-0.29312, 0.95596, -0.01504), (0.00233, -0.01501, -0.99988)
Vector: 98.488, 15.056, 38.913)

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Components

#1: Protein CITRATE SYNTHASE


Mass: 48977.059 Da / Num. of mol.: 2
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-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSECONDARY STRUCTURE SPECIFICATIONS FOR THE PRESENT TETRAGONAL FORM WERE ASSIGNED ON THE BASIS OF ...SECONDARY STRUCTURE SPECIFICATIONS FOR THE PRESENT TETRAGONAL FORM WERE ASSIGNED ON THE BASIS OF THE HIGH RESOLUTION (1.7 ANGSTROMS) MONOCLINIC STRUCTURE. THERE IS VERY LITTLE EVIDENCE FOR SECONDARY STRUCTURAL CHANGE AS A RESULT OF THE OPEN (TETRAGONAL) - CLOSED (MONOCLINIC) TERTIARY STRUCTURAL CHANGE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.36 %
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlcitrate synthase11
20.1 MTris-HCl12
34 mMoxaloacetate12
410 mlS-acetonyl-coenzyme A12
540 %(w/v)polyvinylpyrrolidone12with Tris-HCl
60.45-0.55 Mpotassium/sodium phosphate12

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Data collection

Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 2.95 Å / Num. obs: 18318 / % possible obs: 63.3 % / Num. measured all: 55485 / Rmerge(I) obs: 0.107

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Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 2.9→5 Å / Rfactor Rwork: 0.182
Refinement stepCycle: LAST / Resolution: 2.9→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6888 0 18 96 7002
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.015
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: 2.9 Å / Lowest resolution: 5 Å / Num. reflection obs: 14332 / Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_angle_d

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