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- PDB-1aj8: CITRATE SYNTHASE FROM PYROCOCCUS FURIOSUS -

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Basic information

Entry
Database: PDB / ID: 1aj8
TitleCITRATE SYNTHASE FROM PYROCOCCUS FURIOSUS
ComponentsCITRATE SYNTHASE
KeywordsLYASE / HYPERTHERMOSTABLE
Function / homology
Function and homology information


citrate synthase (unknown stereospecificity) / citrate (Si)-synthase activity / tricarboxylic acid cycle / carbohydrate metabolic process / cytosol
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
CITRIC ACID / COENZYME A / Citrate synthase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRussell, R.J.M. / Ferguson, J.M.C. / Hough, D.W. / Danson, M.J. / Taylor, G.L.
CitationJournal: Biochemistry / Year: 1997
Title: The crystal structure of citrate synthase from the hyperthermophilic archaeon pyrococcus furiosus at 1.9 A resolution,.
Authors: Russell, R.J. / Ferguson, J.M. / Hough, D.W. / Danson, M.J. / Taylor, G.L.
History
DepositionMay 16, 1997Processing site: BNL
Revision 1.0Nov 19, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _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

Downloads & links

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Assembly

Deposited unit
A: CITRATE SYNTHASE
B: CITRATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5996
Polymers84,6802
Non-polymers1,9194
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12620 Å2
ΔGint-21 kcal/mol
Surface area25780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.290, 98.290, 238.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CITRATE SYNTHASE


Mass: 42339.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q53554, EC: 4.1.3.7
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#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.: 482 / 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: 3.39 Å3/Da / Density % sol: 65 %
Crystal growpH: 8
Details: PROTEIN WAS CRYSTALLIZED FROM 0.1M SODIUM CITRATE AND 1.0M AMMONIUM PHOSPHATE., pH 8.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 Msodium citrate1reservoir
21.0 Mammonium phosphate1reservoir
32 mg/mlprotein1drop
420 mMTris-HCl1drop
525 mM1dropKCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9082
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9082 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 848543 / % possible obs: 98.5 % / Redundancy: 9.3 % / Rsym value: 0.039 / Net I/σ(I): 36
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 8.1 / Rsym value: 0.159 / % possible all: 98.2
Reflection
*PLUS
Num. obs: 91136 / Num. measured all: 848543 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.159

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→100 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 -10 %RANDOM
Rwork0.191 ---
obs0.191 91132 98.5 %-
Refinement stepCycle: LAST / Resolution: 1.9→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5690 0 116 482 6288
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2872 -9.4 %
Rwork0.264 9858 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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