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- PDB-5csc: STRUCTURE OF AN OPEN FORM OF CHICKEN HEART CITRATE SYNTHASE AT 2.... -

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Basic information

Entry
Database: PDB / ID: 5csc
TitleSTRUCTURE OF AN OPEN FORM OF CHICKEN HEART CITRATE SYNTHASE AT 2.8 ANGSTROMS RESOLUTION
Components(CITRATE SYNTHASE) x 2
KeywordsOXO-ACID-LYASE
Function / homology
Function and homology information


The tricarboxylic acid cycle / citrate (Si)-synthase / citrate synthase activity / : / citrate metabolic process / tricarboxylic acid cycle / carbohydrate metabolic process / mitochondrial matrix / mitochondrion / 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
Citrate synthase, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsLiao, D.-I. / Karpusas, M. / Remington, S.J.
Citation
Journal: Biochemistry / Year: 1991
Title: Crystal structure of an open conformation of citrate synthase from chicken heart at 2.8-A resolution
Authors: Liao, D.-I. / Karpusas, M. / Remington, S.J.
#1: Journal: J.Mol.Biol. / Year: 1984
Title: Crystal Structure Analysis and Molecular Model of a Complex of Citrate Synthase with Oxaloacetate and S-Acetonyl-Coenzymea
Authors: Wiegand, G. / Remington, S. / Deisenhofer, J. / Huber, R.
#2: 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.
#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.
#4: 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.
History
DepositionMay 7, 1990Processing site: BNL
Revision 1.0Apr 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CITRATE SYNTHASE
B: CITRATE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)94,3042
Polymers94,3042
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.850, 58.850, 259.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
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: (-0.00998, -0.99994, -0.00433), (-0.99993, 0.00995, 0.00688), (-0.00683, 0.0044, -0.99997)
Vector: 86.45081, 85.54562, -0.12062)
DetailsTHE MOLECULE IS A DIMER, WITH ONE DIMER OF MOLECULAR WEIGHT 100000 IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT.

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Components

#1: Protein CITRATE SYNTHASE


Mass: 47322.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P23007, EC: 4.1.3.7
#2: Protein CITRATE SYNTHASE


Mass: 46981.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P23007

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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: 48.29 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop / Details: or 4 degrees centigrade
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.5 Mcitrate1drop
310 mMCoA1drop
41.0 Msodium citrate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 15130 / % possible obs: 62.4 % / Num. measured all: 53801 / Rmerge(I) obs: 0.139
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / % possible obs: 22 %

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.8→6 Å / Rfactor obs: 0.197
Details: THE MODEL WAS FIT USING LIMITED RESOLUTION DATA (2.8 ANGSTROMS) AND THERE IS UNCERTAINTY IN THE SEQUENCE USED IN THIS ANALYSIS (SEE REMARK 4). NOTE, AS A CONSEQUENCE, THAT THERE ARE ...Details: THE MODEL WAS FIT USING LIMITED RESOLUTION DATA (2.8 ANGSTROMS) AND THERE IS UNCERTAINTY IN THE SEQUENCE USED IN THIS ANALYSIS (SEE REMARK 4). NOTE, AS A CONSEQUENCE, THAT THERE ARE DISTANCES, TORSION ANGLES, AND BOND ANGLES IN THIS ENTRY WHICH HAVE VALUES OUTSIDE EXPECTED RANGES.
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6606 0 0 0 6606
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.024
X-RAY DIFFRACTIONt_angle_deg3.3
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd

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