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- PDB-8gi7: C143A variant of Citrate Synthase (CitA) in Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 8gi7
TitleC143A variant of Citrate Synthase (CitA) in Mycobacterium tuberculosis
Componentscitrate synthase (unknown stereospecificity)
KeywordsCYTOSOLIC PROTEIN / Citrate Synthesis / TCA cycle / C143A 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: 3.3 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 13, 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

Downloads & links

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Assembly

Deposited unit
A: citrate synthase (unknown stereospecificity)
B: citrate synthase (unknown stereospecificity)
C: citrate synthase (unknown stereospecificity)
D: citrate synthase (unknown stereospecificity)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,01713
Polymers163,9504
Non-polymers1,0679
Water724
1
A: citrate synthase (unknown stereospecificity)
B: citrate synthase (unknown stereospecificity)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5397
Polymers81,9752
Non-polymers5645
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-44 kcal/mol
Surface area28460 Å2
MethodPISA
2
C: citrate synthase (unknown stereospecificity)
D: citrate synthase (unknown stereospecificity)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4776
Polymers81,9752
Non-polymers5024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9720 Å2
ΔGint-50 kcal/mol
Surface area28290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.001, 254.919, 192.809
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
citrate synthase (unknown stereospecificity)


Mass: 40987.539 Da / Num. of mol.: 4 / Mutation: C143A
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-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 4.68 Å3/Da / Density % sol: 73.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium tartrate dibasic dihydrate, 20% w/v Polyethylene glycol 3,350

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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: Jul 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.3→57.39 Å / Num. obs: 46623 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.1373 / Rpim(I) all: 0.05395 / Rrim(I) all: 0.1477 / Net I/σ(I): 8.42
Reflection shellResolution: 3.3→3.418 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.4316 / Mean I/σ(I) obs: 0.92 / Num. unique obs: 4587 / CC1/2: 0.923 / CC star: 0.98 / Rpim(I) all: 0.1675 / Rrim(I) all: 0.4633 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
DIALSdata scaling
DIALSdata reduction
PHENIX1.18.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→57.39 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2004 1999 4.29 %
Rwork0.1722 --
obs0.1734 46603 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→57.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11199 0 72 4 11275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211543
X-RAY DIFFRACTIONf_angle_d0.49215726
X-RAY DIFFRACTIONf_dihedral_angle_d22.5731716
X-RAY DIFFRACTIONf_chiral_restr0.0381730
X-RAY DIFFRACTIONf_plane_restr0.0052101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.380.32361420.30623165X-RAY DIFFRACTION100
3.38-3.470.26351400.25613140X-RAY DIFFRACTION100
3.47-3.580.28091420.22993155X-RAY DIFFRACTION100
3.58-3.690.24461400.21633117X-RAY DIFFRACTION100
3.69-3.820.24371420.21113164X-RAY DIFFRACTION100
3.82-3.980.23211420.18533170X-RAY DIFFRACTION100
3.98-4.160.20981410.16743154X-RAY DIFFRACTION100
4.16-4.380.18441430.15333174X-RAY DIFFRACTION100
4.38-4.650.16291410.14053171X-RAY DIFFRACTION100
4.65-5.010.17471420.13593194X-RAY DIFFRACTION100
5.01-5.510.15821440.14453187X-RAY DIFFRACTION100
5.51-6.310.21241440.173220X-RAY DIFFRACTION100
6.31-7.950.17171450.15583239X-RAY DIFFRACTION100
7.95-57.390.16581510.15213354X-RAY DIFFRACTION100

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