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

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Basic information

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


citrate synthase (unknown stereospecificity) / citrate 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 ...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
ACETYL COENZYME *A / OXALOACETATE ION / Citrate synthase
Similarity search - Component
Biological speciesMetallosphaera sedula (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 20, 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
B: Citrate synthase
A: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5278
Polymers86,4612
Non-polymers2,0656
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10900 Å2
ΔGint-53 kcal/mol
Surface area28210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.134, 55.973, 76.965
Angle α, β, γ (deg.)83.730, 73.940, 72.220
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-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3O5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C23H38N7O17P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.28 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 22% polyethylene glycol (PEG) 3350 0.2M, potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 50558 / % possible obs: 97.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.045 / Rrim(I) all: 0.088 / Χ2: 2.801 / Net I/σ(I): 13.4 / Num. measured all: 183092
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.40.28124480.90.1770.3331.59596.6
2.03-2.073.40.24925210.9240.1560.2951.66697
2.07-2.113.50.21824830.9340.1350.2571.77797
2.11-2.153.50.1925650.9540.1180.2241.75897.2
2.15-2.23.50.16424800.9660.1020.1941.96597.1
2.2-2.253.50.15925250.9680.0980.1871.88697.5
2.25-2.313.50.1425180.9780.0850.1642.02997.6
2.31-2.373.60.12524940.9810.0770.147297.5
2.37-2.443.60.11725370.9830.0710.1372.1597.7
2.44-2.523.60.11325560.9850.0680.1322.16498
2.52-2.613.60.10625230.9850.0640.1242.39398.1
2.61-2.713.70.09325150.9880.0560.1092.5798
2.71-2.843.70.08325570.9910.050.0972.72598.3
2.84-2.993.70.08225430.990.0490.0953.05698.4
2.99-3.173.70.07825470.9910.0460.0913.36698.7
3.17-3.423.80.06825290.9930.040.0793.60998.8
3.42-3.763.80.06125850.9940.0360.074.36899
3.76-4.313.80.05325630.9950.0320.0624.41899.2
4.31-5.433.80.0525510.9960.030.0584.50499.4
5.43-503.60.05425180.9940.0340.0645.01597.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VGP

1vgp


Resolution: 2→33.35 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.405 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1928 2505 5 %RANDOM
Rwork0.1478 ---
obs0.1499 48053 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 157.21 Å2 / Biso mean: 30.323 Å2 / Biso min: 14.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-1.49 Å2-0.47 Å2
2--0.83 Å20.86 Å2
3----1.87 Å2
Refinement stepCycle: final / Resolution: 2→33.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5942 0 88 328 6358
Biso mean--67.65 39.95 -
Num. residues----743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136176
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175833
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.6568330
X-RAY DIFFRACTIONr_angle_other_deg1.3991.5813524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2155746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69521.25328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.417151134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2821550
X-RAY DIFFRACTIONr_chiral_restr0.0820.2801
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026798
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021322
LS refinement shellResolution: 1.999→2.05 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 206 -
Rwork0.195 3288 -
all-3494 -
obs--92.61 %

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