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- PDB-2csc: Structure of ternary complexes of CITRATE SYNTHASE WITH D-AND L-M... -

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Basic information

Entry
Database: PDB / ID: 2csc
TitleStructure of ternary complexes of CITRATE SYNTHASE WITH D-AND L-MALATE: mechanistic implications
ComponentsCITRATE SYNTHASE
KeywordsLYASE / OXO-ACID-LYASE
Function / homology
Function and homology information


citrate (Si)-synthase / The tricarboxylic acid cycle / citrate synthase activity / citrate (Si)-synthase activity / citrate metabolic process / tricarboxylic acid cycle / carbohydrate metabolic process / mitochondrial matrix / mitochondrion
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-like, small alpha subdomain / Citrate synthase superfamily ...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-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Citrate synthase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBOXYMETHYL COENZYME *A / D-MALATE / Citrate synthase, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsKarpusas, M. / Holland, D. / Remington, S.J.
Citation
Journal: Biochemistry / Year: 1991
Title: 1.9-A structures of ternary complexes of citrate synthase with D- and L-malate: mechanistic implications.
Authors: Karpusas, M. / Holland, D. / 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 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 22, 2012Group: Non-polymer description
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)48,2823
Polymers47,3221
Non-polymers9602
Water1,820101
1
A: CITRATE SYNTHASE
hetero molecules

A: CITRATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5646
Polymers94,6442
Non-polymers1,9194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12820 Å2
ΔGint-61 kcal/mol
Surface area28550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.000, 78.100, 58.300
Angle α, β, γ (deg.)90.00, 78.90, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: SEE REMARK 3.
DetailsTHE MOLECULE IS A DIMER, WITH ONE MONOMER OF MOLECULAR WEIGHT 50000 IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. THE SYMMETRY-RELATED MONOMER CAN BE GENERATED BY THE FOLLOWING CRYSTALLOGRAPHIC TWO-FOLD OPERATION, XS = - XO YS = YO ZS = - ZO WHERE (XO,YO,ZO) ARE THE COORDINATES IN THIS ENTRY AND (XS,YS,ZS) ARE THE SYMMETRY-RELATED SET.

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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: Chemical ChemComp-CMC / CARBOXYMETHYL COENZYME *A


Mass: 825.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O18P3S
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion / Details: referred to 3cts
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

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 25075 / Num. measured all: 52144 / Rmerge(I) obs: 0.098

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.7→6 Å / Rfactor obs: 0.189
Refinement stepCycle: LAST / Resolution: 1.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 61 101 3468
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg2.6
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
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 6 Å / Rfactor all: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_plane_restr0.026

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