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- PDB-1a59: COLD-ACTIVE CITRATE SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 1a59
TitleCOLD-ACTIVE CITRATE SYNTHASE
ComponentsCITRATE SYNTHASE
KeywordsCOLD-ACTIVITY
Function / homology
Function and homology information


2-methylcitrate synthase / 2-methylcitrate synthase activity / propionate metabolic process, methylcitrate cycle / citrate synthase (unknown stereospecificity) / citrate synthase activity / tricarboxylic acid cycle / 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 ...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 / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / COENZYME A / 2-methylcitrate synthase
Similarity search - Component
Biological speciesAntarctic bacterium DS2-3R (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsRussell, R.J.M. / Gerike, U. / Danson, M.J. / Hough, D.W. / Taylor, G.L.
CitationJournal: Structure / Year: 1998
Title: Structural adaptations of the cold-active citrate synthase from an Antarctic bacterium.
Authors: Russell, R.J. / Gerike, U. / Danson, M.J. / Hough, D.W. / Taylor, G.L.
History
DepositionFeb 20, 1998Processing site: BNL
Revision 1.0Mar 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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

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Assembly

Deposited unit
A: CITRATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7093
Polymers41,7491
Non-polymers9602
Water0
1
A: CITRATE SYNTHASE
hetero molecules

A: CITRATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4186
Polymers83,4982
Non-polymers1,9194
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z+2/31
Buried area9330 Å2
ΔGint-39 kcal/mol
Surface area28060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.800, 70.800, 307.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein CITRATE SYNTHASE /


Mass: 41749.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Antarctic bacterium DS2-3R (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O34002
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7

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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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Temperature: 29 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117 mg/mlprotein1drop
2100 mM1dropKCl
320 mMTris-HCl1drop
410 mMCoASH1drop
510 mMcitrate1drop
62.2 Mammonium sulfate1reservoir
720 mMcitrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.909
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997 / Details: COLLIMATOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.909 Å / Relative weight: 1
ReflectionResolution: 2.09→15 Å / Num. obs: 27063 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 23.9
Reflection shellResolution: 2.09→2.16 Å / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 7.7 / Rsym value: 0.12 / % possible all: 88.3
Reflection
*PLUS
Num. measured all: 293261
Reflection shell
*PLUS
% possible obs: 88.3 %

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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: 2.09→100 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 -10 %RANDOM
Rwork0.184 ---
obs0.184 27063 96.2 %-
Refinement stepCycle: LAST / Resolution: 2.09→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 59 0 2951
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.24
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
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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