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- PDB-8gmk: Pyruvate bound structure of Citrate Synthase (CitA) in Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 8gmk
TitlePyruvate bound structure of Citrate Synthase (CitA) in Mycobacterium Tuberculosis
Componentscitrate synthase
KeywordsCYTOSOLIC PROTEIN / Citrate Synthesis / TCA cycle / pyruvate
Function / homology
Function and homology information


citrate synthase (unknown stereospecificity) / citrate (Si)-synthase activity / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PYRUVIC ACID / citrate synthase (unknown stereospecificity)
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsPathirage, R. / Ronning, D. / Yamsek, M.
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 26, 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: citrate synthase
B: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,95127
Polymers82,0392
Non-polymers1,91225
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12860 Å2
ΔGint9 kcal/mol
Surface area27850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.524, 99.524, 141.345
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein citrate synthase


Mass: 41019.605 Da / Num. of mol.: 2
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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Non-polymers , 5 types, 491 molecules

#2: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris pH 8.5, 0.5 M sodium chloride and 19 % w/v polyethylene glycol 3350 in the presence of 5.6 micromolar detergent, CYMAL-6

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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 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.81→41.34 Å / Num. obs: 74189 / % possible obs: 99.87 % / Redundancy: 9.7 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.05 / Rrim(I) all: 0.156 / Χ2: 1.479 / Net I/σ(I): 13.12
Reflection shellResolution: 1.81→1.875 Å / Redundancy: 8.8 % / Rmerge(I) obs: 2.453 / Num. unique obs: 7262 / CC1/2: 0.415 / CC star: 0.766 / Rpim(I) all: 0.863 / Rrim(I) all: 2.603 / Χ2: 0.639 / % possible all: 99.21

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158:000refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→41.34 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2598 2004 2.7 %
Rwork0.2099 --
obs0.212 74189 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5525 0 125 466 6116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095760
X-RAY DIFFRACTIONf_angle_d0.947788
X-RAY DIFFRACTIONf_dihedral_angle_d8.748855
X-RAY DIFFRACTIONf_chiral_restr0.056851
X-RAY DIFFRACTIONf_plane_restr0.011031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.850.47651410.41384971X-RAY DIFFRACTION98
1.85-1.90.43141400.37145106X-RAY DIFFRACTION100
1.9-1.960.33431430.33645128X-RAY DIFFRACTION100
1.96-2.020.33041430.2995097X-RAY DIFFRACTION100
2.02-2.10.32251420.28225129X-RAY DIFFRACTION100
2.1-2.180.31511410.2545155X-RAY DIFFRACTION100
2.18-2.280.29311440.25525112X-RAY DIFFRACTION100
2.28-2.40.28011410.22485143X-RAY DIFFRACTION100
2.4-2.550.25941430.23855158X-RAY DIFFRACTION100
2.55-2.750.29711420.20935153X-RAY DIFFRACTION100
2.75-3.020.27441460.23065201X-RAY DIFFRACTION100
3.02-3.460.26671430.20065198X-RAY DIFFRACTION100
3.46-4.360.21921430.17345256X-RAY DIFFRACTION100
4.36-41.340.20781520.165443X-RAY DIFFRACTION100

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