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- PDB-8gmf: R153M variant of Citrate Synthase (CitA) in Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 8gmf
TitleR153M variant of Citrate Synthase (CitA) in Mycobacterium tuberculosis
Componentscitrate synthase
KeywordsCYTOSOLIC PROTEIN / Citrate Synthesis / TCA cycle / R153M variant
Function / homology
Function and homology information


citrate synthase (unknown stereospecificity) / citrate synthase activity / tricarboxylic acid cycle
Similarity search - Function
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
Similarity search - Domain/homology
citrate synthase (unknown stereospecificity)
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsPathirage, R. / Ronning, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)CA260749 United States
CitationJournal: Rsc Med Chem / Year: 2023
Title: Mycobacterium tuberculosis CitA activity is modulated by cysteine oxidation and pyruvate binding.
Authors: Pathirage, R. / Favrot, L. / Petit, C. / Yamsek, M. / Singh, S. / Mallareddy, J.R. / Rana, S. / Natarajan, A. / Ronning, D.R.
History
DepositionMar 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: citrate synthase
B: citrate synthase
C: citrate synthase
D: citrate synthase
E: citrate synthase
F: citrate synthase
G: citrate synthase
H: citrate synthase


Theoretical massNumber of molelcules
Total (without water)321,3188
Polymers321,3188
Non-polymers00
Water0
1
A: citrate synthase
C: citrate synthase


Theoretical massNumber of molelcules
Total (without water)80,3292
Polymers80,3292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-65 kcal/mol
Surface area29670 Å2
MethodPISA
2
B: citrate synthase
F: citrate synthase


Theoretical massNumber of molelcules
Total (without water)80,3292
Polymers80,3292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-65 kcal/mol
Surface area29640 Å2
MethodPISA
3
D: citrate synthase
E: citrate synthase


Theoretical massNumber of molelcules
Total (without water)80,3292
Polymers80,3292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-64 kcal/mol
Surface area29730 Å2
MethodPISA
4
G: citrate synthase
H: citrate synthase


Theoretical massNumber of molelcules
Total (without water)80,3292
Polymers80,3292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-64 kcal/mol
Surface area30300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.906, 129.906, 256.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
citrate synthase /


Mass: 40164.738 Da / Num. of mol.: 8 / Mutation: R153M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: citA, SAMEA2683035_02214 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A045JB88, citrate synthase (unknown stereospecificity)

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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: 3.3 Å3/Da / Density % sol: 62.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Magnesium chloride, 20 w/v % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.96→91.86 Å / Num. obs: 88181 / % possible obs: 99.77 % / Redundancy: 7.8 % / Biso Wilson estimate: 75.64 Å2 / CC1/2: 0.986 / CC star: 0.997 / Rmerge(I) obs: 0.2313 / Rpim(I) all: 0.08896 / Rrim(I) all: 0.2479 / Χ2: 1.898 / Net I/σ(I): 5.2
Reflection shellResolution: 2.96→3.066 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.602 / Num. unique obs: 8796 / CC1/2: 0.606 / CC star: 0.869 / Rpim(I) all: 0.6152 / Rrim(I) all: 1.717 / % possible all: 98.33

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158:000refinement
DIALSdata scaling
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.96→91.83 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2569 3351 1.93 %
Rwork0.2098 --
obs0.2107 88181 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.96→91.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22313 0 0 0 22313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222822
X-RAY DIFFRACTIONf_angle_d0.46131090
X-RAY DIFFRACTIONf_dihedral_angle_d3.633258
X-RAY DIFFRACTIONf_chiral_restr0.0373443
X-RAY DIFFRACTIONf_plane_restr0.0044140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.96-30.37381260.33736302X-RAY DIFFRACTION89
3-3.050.39611380.33246912X-RAY DIFFRACTION97
3.05-3.090.36311390.327077X-RAY DIFFRACTION98
3.09-3.150.33411320.30916997X-RAY DIFFRACTION99
3.15-3.20.3891380.33477144X-RAY DIFFRACTION100
3.2-3.260.34621460.30787206X-RAY DIFFRACTION100
3.26-3.320.36291360.29447095X-RAY DIFFRACTION100
3.32-3.390.32841420.27337151X-RAY DIFFRACTION100
3.39-3.460.2611400.2647142X-RAY DIFFRACTION100
3.46-3.540.35141400.24427106X-RAY DIFFRACTION100
3.54-3.630.31061400.23567174X-RAY DIFFRACTION100
3.63-3.730.31061360.22377188X-RAY DIFFRACTION100
3.73-3.840.28861360.22187163X-RAY DIFFRACTION100
3.84-3.960.27791440.20827107X-RAY DIFFRACTION100
3.96-4.10.2471420.19287140X-RAY DIFFRACTION100
4.1-4.270.21861380.17957154X-RAY DIFFRACTION100
4.27-4.460.2591460.18497152X-RAY DIFFRACTION100
4.46-4.70.1921420.17967113X-RAY DIFFRACTION100
4.7-4.990.21141460.17567190X-RAY DIFFRACTION100
4.99-5.380.18041540.18217129X-RAY DIFFRACTION100
5.38-5.920.24091360.20497141X-RAY DIFFRACTION100
5.92-6.780.25521340.20177148X-RAY DIFFRACTION100
6.78-8.530.22621440.16777128X-RAY DIFFRACTION100

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