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- PDB-8gmi: Citrate Synthase (CitA) in Mycobacterium tuberculosis modified by... -

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Basic information

Entry
Database: PDB / ID: 8gmi
TitleCitrate Synthase (CitA) in Mycobacterium tuberculosis modified by Ebselen at C143 residue
Componentscitrate synthase
KeywordsCYTOSOLIC PROTEIN / Citrate Synthesis / TCA cycle / cysteine modified by Ebselen
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
N-phenyl-2-selanylbenzamide / CITRATE ANION / 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 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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
C: citrate synthase
D: citrate synthase
E: citrate synthase
F: citrate synthase
G: citrate synthase
H: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,31221
Polymers328,1578
Non-polymers3,15513
Water2,126118
1
A: citrate synthase
B: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7815
Polymers82,0392
Non-polymers7413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-60 kcal/mol
Surface area29480 Å2
MethodPISA
2
C: citrate synthase
D: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9706
Polymers82,0392
Non-polymers9314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9000 Å2
ΔGint-57 kcal/mol
Surface area29070 Å2
MethodPISA
3
E: citrate synthase
F: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9706
Polymers82,0392
Non-polymers9314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9270 Å2
ΔGint-60 kcal/mol
Surface area28770 Å2
MethodPISA
4
G: citrate synthase
H: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5924
Polymers82,0392
Non-polymers5522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-58 kcal/mol
Surface area29210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.017, 167.486, 220.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
citrate synthase


Mass: 41019.605 Da / Num. of mol.: 8
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-9JT / N-phenyl-2-selanylbenzamide / ~{N}-phenyl-2-selanyl-benzamide / Ebselen, bound form


Mass: 276.193 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C13H11NOSe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.44 Å3/Da / Density % sol: 64.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium sulfate, 0.1 M HEPES pH 7.5 and 25 % 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: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.7→63.06 Å / Num. obs: 124596 / % possible obs: 99.91 % / Redundancy: 7.6 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.224 / Rpim(I) all: 0.08717 / Rrim(I) all: 0.2406 / Net I/σ(I): 6.79
Reflection shellResolution: 2.7→2.797 Å / Num. unique obs: 12322 / CC1/2: 0.476 / CC star: 0.803

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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→63.06 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2532 1828 1.47 %
Rwork0.2142 --
obs0.2212 124507 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→63.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22391 0 65 118 22574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222972
X-RAY DIFFRACTIONf_angle_d0.44731291
X-RAY DIFFRACTIONf_dihedral_angle_d6.6743349
X-RAY DIFFRACTIONf_chiral_restr0.0373434
X-RAY DIFFRACTIONf_plane_restr0.0044170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.45891380.44549266X-RAY DIFFRACTION99
2.77-2.850.44081390.37789310X-RAY DIFFRACTION100
2.85-2.950.34571390.33259348X-RAY DIFFRACTION100
2.95-3.050.35791400.2919416X-RAY DIFFRACTION100
3.05-3.170.32751390.27859297X-RAY DIFFRACTION100
3.17-3.320.31511390.29229384X-RAY DIFFRACTION100
3.32-3.490.30321410.29239411X-RAY DIFFRACTION100
3.49-3.710.23011400.21879413X-RAY DIFFRACTION100
3.71-40.2441410.20059437X-RAY DIFFRACTION100
4-4.40.22211410.18359456X-RAY DIFFRACTION100
4.4-5.040.19791410.16589505X-RAY DIFFRACTION100
5.04-6.350.25811420.19079553X-RAY DIFFRACTION100
6.35-63.060.21391480.16689883X-RAY DIFFRACTION100

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