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- PDB-6abw: Crystal structure of citrate synthase (Msed_0281) from Metallosph... -

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Basic information

Entry
Database: PDB / ID: 6abw
TitleCrystal structure of citrate synthase (Msed_0281) from Metallosphaera sedula in complex with acetyl-CoA
ComponentsCitrate synthase
KeywordsTRANSFERASE / Citrate synthase / Metallosphaera sedula
Function / homology
Function and homology information


citrate synthase (unknown stereospecificity) / citrate synthase activity / tricarboxylic acid cycle / membrane / 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 / Citrate synthase
Similarity search - Component
Biological speciesMetallosphaera sedula (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsLee, S.-H. / Kim, K.-J.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Crystal structure and biochemical properties of msed_0281, the citrate synthase from Metallosphaera sedula.
Authors: Lee, S.H. / Kim, K.J.
History
DepositionJul 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7554
Polymers43,7611
Non-polymers9943
Water4,396244
1
A: Citrate synthase
hetero molecules

A: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5098
Polymers87,5222
Non-polymers1,9886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area10680 Å2
ΔGint-38 kcal/mol
Surface area28000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.609, 94.806, 129.863
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-730-

HOH

21A-738-

HOH

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Components

#1: Protein Citrate synthase /


Mass: 43760.926 Da / Num. of mol.: 1
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_0281 / Production host: Escherichia coli (E. coli)
References: UniProt: A4YDF6, citrate synthase (unknown stereospecificity)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 35% v/v (+/-)-2-Methyl-2,4- pentandiol (MPD), 0.1 M Bis-Tris, pH 5.0, 0.2 M ammonium acetate

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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: May 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.72→64.94 Å / Num. obs: 39803 / % possible obs: 98.1 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 40.3
Reflection shellResolution: 1.72→1.75 Å / Rmerge(I) obs: 0.293 / Num. unique obs: 1928

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GVM

1gvm


Resolution: 1.72→64.93 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.164 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.101
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 1971 5 %RANDOM
Rwork0.1499 ---
obs0.1522 37819 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 109.41 Å2 / Biso mean: 21.223 Å2 / Biso min: 6.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20 Å2
2--1.63 Å20 Å2
3----0.7 Å2
Refinement stepCycle: final / Resolution: 1.72→64.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2920 0 63 244 3227
Biso mean--41.68 32.75 -
Num. residues----369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193050
X-RAY DIFFRACTIONr_bond_other_d0.0020.022862
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.9914135
X-RAY DIFFRACTIONr_angle_other_deg1.06436626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8995368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61623.385130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83115515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2991519
X-RAY DIFFRACTIONr_chiral_restr0.1990.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213331
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02637
LS refinement shellResolution: 1.723→1.768 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 153 -
Rwork0.228 2650 -
all-2803 -
obs--94.16 %

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