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- PDB-3cts: CRYSTALLOGRAPHIC REFINEMENT AND ATOMIC MODELS OF TWO DIFFERENT FO... -

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Basic information

Entry
Database: PDB / ID: 3cts
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 / homologyCITRIC ACID / COENZYME A
Function and homology information
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 1.7 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 25, 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 21, 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

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Assembly

Deposited unit
A: CITRATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1683
Polymers37,2091
Non-polymers9602
Water1,820101
1
A: CITRATE SYNTHASE
hetero molecules

A: CITRATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3376
Polymers74,4182
Non-polymers1,9194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12570 Å2
ΔGint-6 kcal/mol
Surface area29270 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.
2: RESIDUES 83, 292 AND 434 CONSIST OF ONLY ONE ATOM, N. NONE OF THESE ARE EXPLICIT DISCONTINUITIES, BUT MERELY CORRESPOND TO POORLY DEFINED REGIONS WHICH HAVE BEEN OMITTED.

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Components

#1: Protein CITRATE SYNTHASE /


Mass: 37208.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Tissue: HEART MUSCLE / References: EC: 4.1.3.7
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


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


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


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF CHICKEN HEART CITRATE SYNTHASE HAS NOT BEEN DETERMINED. IT IS EXPECTED TO BE HIGHLY ...THE SEQUENCE OF CHICKEN HEART CITRATE SYNTHASE HAS NOT BEEN DETERMINED. IT IS EXPECTED TO BE HIGHLY HOMOLOGOUS TO THE SEQUENCE OF THE PIG HEART ENZYME. THE SEQUENCE FOR THE PIG ENZYME WAS USED AS A GUIDE IN BUILDING THIS MODEL.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.74 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.0 mg/mlprotein1drop
20.9 %sodium citrate1drop
31 mMCoA1drop
41.2 Msodium citrate 1reservoir

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Data collection

Reflection
*PLUS

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Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 1.7→5 Å / Rfactor Rwork: 0.192
Refinement stepCycle: LAST / Resolution: 1.7→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 59 101 3469
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_deg2.9
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
Rfactor obs: 0.192 / Highest resolution: 1.7 Å / Lowest resolution: 5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_angle_d / Dev ideal: 2.9

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