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- PDB-8s97: C143W variant of Citrate Synthase (CitA) in Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 8s97
TitleC143W variant of Citrate Synthase (CitA) in Mycobacterium tuberculosis
Componentscitrate synthase
KeywordsCYTOSOLIC PROTEIN / Citrate Synthesis / TCA cycle / C143W 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
Putative citrate synthase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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)41,3515
Polymers41,1031
Non-polymers2484
Water34219
1
A: citrate synthase
hetero molecules

A: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,70210
Polymers82,2052
Non-polymers4978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_554-y+1/2,-x+1/2,-z-1/21
Buried area9440 Å2
ΔGint-35 kcal/mol
Surface area28870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.472, 148.472, 230.402
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: 41102.672 Da / Num. of mol.: 1 / Mutation: C143W
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.: 4 / Source method: isolated from a natural source / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 7.72 Å3/Da / Density % sol: 84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium Acetate pH 4.5, 3 M NaCl with the additive 5 % w/v D-sorbitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 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: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.7→50.5 Å / Num. obs: 35636 / % possible obs: 99.81 % / Redundancy: 15 % / CC1/2: 0.993 / Rmerge(I) obs: 0.2238 / Rpim(I) all: 0.05985 / Rrim(I) all: 0.2317 / Net I/σ(I): 5.78
Reflection shellResolution: 2.7→2.797 Å / Rmerge(I) obs: 1.774 / Num. unique obs: 3488 / CC1/2: 0.639 / Rpim(I) all: 0.4694 / Rrim(I) all: 1.836

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158:000refinement
DIALSdata scaling
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→50.5 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2716 3022 4.5 %
Rwork0.2431 --
obs0.2444 35636 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→50.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 16 19 2831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022873
X-RAY DIFFRACTIONf_angle_d0.4813906
X-RAY DIFFRACTIONf_dihedral_angle_d3.456412
X-RAY DIFFRACTIONf_chiral_restr0.039429
X-RAY DIFFRACTIONf_plane_restr0.004519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.740.34371260.39682570X-RAY DIFFRACTION88
2.74-2.790.44621400.38482878X-RAY DIFFRACTION97
2.79-2.840.37691380.3782892X-RAY DIFFRACTION100
2.84-2.890.3741390.36752950X-RAY DIFFRACTION100
2.89-2.940.33551380.34962926X-RAY DIFFRACTION100
2.94-30.35331380.3382929X-RAY DIFFRACTION100
3-3.070.39331360.33852928X-RAY DIFFRACTION100
3.07-3.140.36781360.30782915X-RAY DIFFRACTION100
3.14-3.220.35651390.31232936X-RAY DIFFRACTION100
3.22-3.30.3211410.29092951X-RAY DIFFRACTION100
3.3-3.40.27541360.25792917X-RAY DIFFRACTION100
3.4-3.510.3131390.24762937X-RAY DIFFRACTION100
3.51-3.640.27791390.23832939X-RAY DIFFRACTION100
3.64-3.780.2931400.23512922X-RAY DIFFRACTION100
3.78-3.950.23031350.22372937X-RAY DIFFRACTION100
3.95-4.160.3071310.20712953X-RAY DIFFRACTION100
4.16-4.420.19871400.19882917X-RAY DIFFRACTION100
4.42-4.760.23791390.19592937X-RAY DIFFRACTION100
4.77-5.240.24911370.21192931X-RAY DIFFRACTION100
5.24-60.2191380.21182938X-RAY DIFFRACTION100
6-7.560.21451400.22632932X-RAY DIFFRACTION100
7.56-50.50.23871370.21022949X-RAY DIFFRACTION100

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