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- PDB-6csc: CHICKEN CITRATE SYNTHASE COMPLEX WITH TRIFLUOROACETONYL-COA AND C... -

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Basic information

Entry
Database: PDB / ID: 6csc
TitleCHICKEN CITRATE SYNTHASE COMPLEX WITH TRIFLUOROACETONYL-COA AND CITRATE
ComponentsCITRATE SYNTHASE
KeywordsOXO-ACID-LYASE / TRICARBOXYLIC ACID CYCLE / ALLOSTERIC ENZYME
Function / homology
Function and homology information


citrate (Si)-synthase / The tricarboxylic acid cycle / 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
CITRIC ACID / TRIFLUOROACETONYL COENZYME A / Citrate synthase, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsUsher, K.C. / Remington, S.J.
Citation
Journal: To be Published
Title: Trifluoroacetonyl Coenzyme A, an Inhibitor of Citrate Synthase, Binds in a Combination of Productive and Nonproductive Modes
Authors: Usher, K.C. / Branchaud, B. / Remington, S.J.
#1: Journal: Biochemistry / Year: 1994
Title: A Very Short Hydrogen Bond Provides Only Moderate Stabilization of an Enzyme-Inhibitor Complex of Citrate Synthase
Authors: Usher, K.C. / Remington, S.J. / Martin, D.P. / Drueckhammer, D.G.
#2: 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.
#3: 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.
History
DepositionJun 19, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: 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 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)98,8066
Polymers96,6662
Non-polymers2,1394
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13070 Å2
ΔGint-43 kcal/mol
Surface area28250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.370, 100.210, 87.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.14515, -0.30364, 0.94166), (-0.30204, -0.8927, -0.33442), (0.94217, -0.33297, 0.03786)
Vector: 36.16176, 66.97815, -11.28015)

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Components

#1: Protein CITRATE SYNTHASE


Mass: 48333.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cellular location: INNER MATRIX / Organ: HEART / Organelle: MITOCHONDRIA / Tissue: MUSCLE / References: UniProt: P23007, EC: 4.1.3.7
#2: Chemical ChemComp-COF / TRIFLUOROACETONYL COENZYME A


Mass: 877.569 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H37F3N7O17P3S
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 55 %
Crystal growpH: 6
Details: CRYSTALLIZED FROM 1.05M NA CITRATE, PH 6.0 2 MM TRIFLUOROACETONYL COENZYME A

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jan 15, 1993 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.23→25 Å / Num. obs: 40589 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 9.1
Reflection shellResolution: 2.23→2.4 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 2.5 / % possible all: 51

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Processing

Software
NameVersionClassification
FASTRANmodel building
ROTFUNmodel building
TNT5Frefinement
SDMS(DCREDUCE)data reduction
SDMS(SCALE)data scaling
FASTRANphasing
ROTFUNphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CSC

1csc


Resolution: 2.25→25 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.158 --
all-40478 -
obs-40478 86 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 478 Å2 / ksol: 0.99 e/Å3
Refinement stepCycle: LAST / Resolution: 2.25→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6787 0 168 146 7101
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01471271
X-RAY DIFFRACTIONt_angle_deg2.396452
X-RAY DIFFRACTIONt_dihedral_angle_d18.240970
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0191601
X-RAY DIFFRACTIONt_gen_planes0.01510275
X-RAY DIFFRACTIONt_it6.269571
X-RAY DIFFRACTIONt_nbd0.0179720

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