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- PDB-6abx: Crystal structure of citrate synthase (Msed_1522) from Metallosph... -

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Basic information

Entry
Database: PDB / ID: 6abx
TitleCrystal structure of citrate synthase (Msed_1522) from Metallosphaera sedula in complex with citrate
ComponentsCitrate synthase
KeywordsTRANSFERASE / Citrate synthase / Metallosphaera sedula
Function / homology
Function and homology information


citrate synthase activity / citrate synthase (unknown stereospecificity) / 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 ...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
CITRATE ANION / Citrate synthase
Similarity search - Component
Biological speciesMetallosphaera sedula (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLee, S.-H. / Son, H.-F. / Kim, K.-J.
CitationJournal: PLoS ONE / Year: 2019
Title: Structural insights into the inhibition properties of archaeon citrate synthase from Metallosphaera sedula.
Authors: Lee, S.H. / Son, H.F. / Kim, K.J.
History
DepositionJul 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Citrate synthase
B: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1167
Polymers86,4612
Non-polymers6545
Water10,683593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10680 Å2
ΔGint-40 kcal/mol
Surface area27390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.181, 53.522, 76.285
Angle α, β, γ (deg.)93.560, 105.730, 102.160
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Citrate synthase


Mass: 43230.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Metallosphaera sedula (strain ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2) (archaea)
Strain: ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2 / Gene: Msed_1522 / Production host: Escherichia coli (E. coli)
References: UniProt: A4YGX6, citrate synthase (unknown stereospecificity)
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 800mM sodium phosphate monobasic/1200mM potassium phosphate dibasic, 0.1 M sodium acetate/acetic acid pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.7→72.84 Å / Num. obs: 79198 / % possible obs: 97.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 22
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.263 / Num. unique obs: 1703

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VGP

1vgp


Resolution: 1.7→29.15 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.847 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.093
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1803 3916 4.9 %RANDOM
Rwork0.1443 ---
obs0.1461 75282 96.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.2 Å2 / Biso mean: 21.068 Å2 / Biso min: 3.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20.89 Å20.11 Å2
2--0.68 Å20.43 Å2
3----0.96 Å2
Refinement stepCycle: final / Resolution: 1.7→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5918 0 44 593 6555
Biso mean--30.17 33.99 -
Num. residues----740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0146073
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175576
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.6638177
X-RAY DIFFRACTIONr_angle_other_deg1.0821.63813084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9875738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45921.235324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.261151122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4681550
X-RAY DIFFRACTIONr_chiral_restr0.1620.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026750
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021106
LS refinement shellResolution: 1.698→1.742 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 276 -
Rwork0.205 5256 -
all-5532 -
obs--91.38 %

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