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- PDB-8s9d: C143S variant of Citrate Synthase (CitA) in Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 8s9d
TitleC143S variant of Citrate Synthase (CitA) in Mycobacterium tuberculosis
Componentscitrate synthase
KeywordsCYTOSOLIC PROTEIN / Citrate Synthesis / TCA cycle / C143S variant
Function / homology
Function and homology information


citrate synthase (unknown stereospecificity) / : / tricarboxylic acid cycle / carbohydrate metabolic process / cytosol
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 ANION / Putative citrate synthase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 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 27, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5037
Polymers41,0041
Non-polymers4996
Water48627
1
A: citrate synthase
hetero molecules

A: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,00614
Polymers82,0072
Non-polymers99912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_554-y+1/2,-x+1/2,-z-1/21
Buried area10240 Å2
ΔGint-35 kcal/mol
Surface area29120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.253, 150.253, 231.657
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein citrate synthase


Mass: 41003.539 Da / Num. of mol.: 1 / Mutation: C143S
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)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C2H6O2
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 7.97 Å3/Da / Density % sol: 84.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Sodium Acetate pH 4.5, 3 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.57→50.85 Å / Num. obs: 42440 / % possible obs: 99.89 % / Redundancy: 15 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.1836 / Rpim(I) all: 0.04913 / Rrim(I) all: 0.1902 / Net I/σ(I): 9.63
Reflection shellResolution: 2.57→2.662 Å / Redundancy: 15.1 % / Rmerge(I) obs: 2.962 / Num. unique obs: 4186 / CC1/2: 0.63 / CC star: 0.879 / Rpim(I) all: 0.787 / Rrim(I) all: 3.065 / % possible all: 99.62

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158:000refinement
DIALSdata scaling
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→50.85 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.329 3523 4.38 %
Rwork0.3133 --
obs0.316 42440 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.57→50.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2788 0 33 27 2848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042878
X-RAY DIFFRACTIONf_angle_d0.5813910
X-RAY DIFFRACTIONf_dihedral_angle_d5.2418
X-RAY DIFFRACTIONf_chiral_restr0.04429
X-RAY DIFFRACTIONf_plane_restr0.007521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.610.48621270.48452913X-RAY DIFFRACTION94
2.61-2.640.46711580.45623019X-RAY DIFFRACTION99
2.64-2.680.42641410.38513064X-RAY DIFFRACTION99
2.68-2.720.35481310.3773098X-RAY DIFFRACTION99
2.72-2.770.35341330.34073077X-RAY DIFFRACTION100
2.77-2.820.33961340.34953115X-RAY DIFFRACTION100
2.82-2.870.31911530.34523041X-RAY DIFFRACTION100
2.87-2.920.37991460.34793081X-RAY DIFFRACTION100
2.92-2.980.38881340.34673075X-RAY DIFFRACTION100
2.98-3.050.38531360.36263069X-RAY DIFFRACTION100
3.05-3.120.33711510.37743088X-RAY DIFFRACTION100
3.12-3.20.39961330.36713112X-RAY DIFFRACTION100
3.2-3.280.35581540.34923039X-RAY DIFFRACTION100
3.28-3.380.38211290.33693103X-RAY DIFFRACTION100
3.38-3.490.34781520.33383111X-RAY DIFFRACTION100
3.49-3.610.34381470.30683060X-RAY DIFFRACTION100
3.61-3.760.31311290.3023088X-RAY DIFFRACTION100
3.76-3.930.34571360.29593113X-RAY DIFFRACTION100
3.93-4.130.31851440.29043077X-RAY DIFFRACTION100
4.14-4.390.33811490.29683060X-RAY DIFFRACTION100
4.39-4.730.30181420.28383094X-RAY DIFFRACTION100
4.73-5.210.28381310.26693103X-RAY DIFFRACTION100
5.21-5.960.331450.30363075X-RAY DIFFRACTION100
5.96-7.510.29781610.30293068X-RAY DIFFRACTION100
7.51-50.850.27281270.29673098X-RAY DIFFRACTION100

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