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

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Basic information

Entry
Database: PDB / ID: 6abv
TitleCrystal structure of citrate synthase (Msed_0281) from Metallosphaera sedula
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 / 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 ...: / 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
Biological speciesMetallosphaera sedula (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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)43,8143
Polymers43,6301
Non-polymers1842
Water3,351186
1
A: Citrate synthase
hetero molecules

A: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6286
Polymers87,2592
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area8220 Å2
ΔGint-48 kcal/mol
Surface area28120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.711, 93.622, 130.228
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Citrate synthase


Mass: 43629.734 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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 35% v/v (+/-)-2-Methyl-2,4- pentandiol (MPD), 0.1 M Bis-Tris, pH 5.0, and 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: 1.8→65.12 Å / Num. obs: 34475 / % possible obs: 98 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 45.7
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.308 / Num. unique obs: 1703

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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: 1.8→65.11 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.514 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.127
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2234 1743 5.1 %RANDOM
Rwork0.1827 ---
obs0.1848 32700 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 93.44 Å2 / Biso mean: 27.804 Å2 / Biso min: 10.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å2-0 Å2-0 Å2
2--2.69 Å20 Å2
3----1.6 Å2
Refinement stepCycle: final / Resolution: 1.8→65.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2903 0 12 186 3101
Biso mean--26.05 40.93 -
Num. residues----367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192980
X-RAY DIFFRACTIONr_bond_other_d0.0020.022820
X-RAY DIFFRACTIONr_angle_refined_deg1.9711.9724033
X-RAY DIFFRACTIONr_angle_other_deg1.09536527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1045366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.52623.281128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39815512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9691519
X-RAY DIFFRACTIONr_chiral_restr0.1230.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213278
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02625
LS refinement shellResolution: 1.803→1.85 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 139 -
Rwork0.226 2383 -
all-2522 -
obs--98.63 %

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