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- PDB-1o7x: Citrate synthase from Sulfolobus solfataricus -

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Basic information

Entry
Database: PDB / ID: 1o7x
TitleCitrate synthase from Sulfolobus solfataricus
ComponentsCITRATE SYNTHASE
KeywordsSYNTHASE / LYASE / TRICARBOXYLIC ACID CYCLE
Function / homology
Function and homology information


citrate synthase (unknown stereospecificity) / citrate (Si)-synthase activity / tricarboxylic acid cycle / carbohydrate metabolic process / cytoplasm
Similarity search - Function
2-methylcitrate synthase/citrate synthase type I / Citrate synthase, bacterial-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 ...2-methylcitrate synthase/citrate synthase type I / Citrate synthase, bacterial-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
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBell, G.S. / Russell, R.J.M. / Connaris, H. / Hough, D.W. / Danson, M.J. / Taylor, G.L.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: Stepwise Adaptations of Citrate Synthase to Survival at Life'S Extremes. From Psychrophile to Hyperthermophile.
Authors: Bell, G.S. / Russell, R.J.M. / Connaris, H. / Hough, D.W. / Danson, M.J. / Taylor, G.L.
History
DepositionNov 19, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 30, 2018Group: Data collection / Category: diffrn_detector
Revision 1.4May 8, 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

Downloads & links

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Assembly

Deposited unit
A: CITRATE SYNTHASE
B: CITRATE SYNTHASE
C: CITRATE SYNTHASE
D: CITRATE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)171,2244
Polymers171,2244
Non-polymers00
Water00
1
A: CITRATE SYNTHASE
B: CITRATE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)85,6122
Polymers85,6122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: CITRATE SYNTHASE
D: CITRATE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)85,6122
Polymers85,6122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)77.340, 97.860, 119.330
Angle α, β, γ (deg.)90.00, 107.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CITRATE SYNTHASE


Mass: 42806.059 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P80148, EC: 4.1.3.7
Compound detailsCITRATE SYNTHASE IS FOUND IN THOSE CELLS CAPABLE OF OXIDATIVE METABOLISM.

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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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growpH: 7.2 / Details: pH 7.20
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMcitrate1dropand CoA
3100 mMTris-HCl1reservoirpH7.2
417 %(v/v)PEG80001reservoir
50.1 M1reservoirCaCl2

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF NONIUS / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 46758 / % possible obs: 88.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.4
Reflection shellResolution: 2.71→2.82 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 3.2 / % possible all: 91.2
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 148169
Reflection shell
*PLUS
% possible obs: 91.2 % / Mean I/σ(I) obs: 3.25

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Processing

SoftwareName: REFMAC / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→20 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.285 -10 %RANDOM
Rwork0.208 ---
obs0.208 46758 88.6 %-
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11738 0 0 0 11738
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d0.032

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