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- PDB-1cts: CRYSTALLOGRAPHIC REFINEMENT AND ATOMIC MODELS OF TWO DIFFERENT FO... -

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Basic information

Entry
Database: PDB / ID: 1cts
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 / 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
CITRIC ACID / Citrate synthase, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.7 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 7, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1692
Polymers48,9771
Non-polymers1921
Water00
1
A: CITRATE SYNTHASE
hetero molecules

A: CITRATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3384
Polymers97,9542
Non-polymers3842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area9270 Å2
ΔGint-55 kcal/mol
Surface area32600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.400, 77.400, 196.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
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: 48977.059 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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
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: 3 Å3/Da / Density % sol: 59.02 %
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlprotein1drop
21.35 Msodium/potassium phosphate1drop
32 mMATP1drop
41.55 Msodium/potassium phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 2.7→5 Å / Rfactor Rwork: 0.183
Refinement stepCycle: LAST / Resolution: 2.7→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3444 0 13 0 3457
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.013
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: 2.7 Å / Lowest resolution: 5 Å / Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_angle_d / Dev ideal: 2.6

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