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- PDB-8gm9: Structure of Citrate Synthase(CitA) in Mycobacterium Tuberculosis -

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Basic information

Entry
Database: PDB / ID: 8gm9
TitleStructure of Citrate Synthase(CitA) in Mycobacterium Tuberculosis
Componentscitrate synthase
KeywordsCYTOSOLIC PROTEIN / Citrate Synthesis / TCA cycle
Function / homology
Function and homology information


citrate synthase (unknown stereospecificity) / citrate 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
ACRYLIC ACID / DI(HYDROXYETHYL)ETHER / Putative citrate synthase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPathirage, R. / Ronning, D. / Favrot, L.
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 24, 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
B: citrate synthase
C: citrate synthase
D: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,43023
Polymers164,0784
Non-polymers1,35119
Water3,927218
1
A: citrate synthase
D: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,72412
Polymers82,0392
Non-polymers68510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-29 kcal/mol
Surface area27610 Å2
MethodPISA
2
B: citrate synthase
C: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,70611
Polymers82,0392
Non-polymers6679
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-44 kcal/mol
Surface area26950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.330, 121.033, 99.584
Angle α, β, γ (deg.)90.00, 94.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
citrate synthase


Mass: 41019.605 Da / Num. of mol.: 4
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.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-AKR / ACRYLIC ACID


Mass: 72.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.02 M magnesium chloride, 0.1 M HEPES pH 7.5, and 22 % w/v poly(acrylic acid sodium salt) 5100, 0.1 M barium chloride

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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: Nov 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.4→43.06 Å / Num. obs: 65711 / % possible obs: 94.26 % / Redundancy: 3.5 % / CC1/2: 0.982 / CC star: 0.995 / Rmerge(I) obs: 0.1686 / Rpim(I) all: 0.1063 / Rrim(I) all: 0.2 / Net I/σ(I): 6.93
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.057 / Num. unique obs: 6925 / CC1/2: 0.681 / CC star: 0.9 / Rpim(I) all: 0.6311 / Rrim(I) all: 1.233 / % possible all: 99.77

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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: 2.4→43.06 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2751 1521 2.32 %
Rwork0.2197 --
obs0.2209 65574 94.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10921 0 89 218 11228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211249
X-RAY DIFFRACTIONf_angle_d0.44315279
X-RAY DIFFRACTIONf_dihedral_angle_d4.3161626
X-RAY DIFFRACTIONf_chiral_restr0.0361683
X-RAY DIFFRACTIONf_plane_restr0.0052031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.38761650.33926096X-RAY DIFFRACTION100
2.48-2.570.35981500.30586142X-RAY DIFFRACTION100
2.57-2.670.33451360.27456136X-RAY DIFFRACTION100
2.67-2.790.33441450.25716196X-RAY DIFFRACTION100
2.79-2.940.29631400.25686097X-RAY DIFFRACTION99
2.94-3.120.28361420.24546128X-RAY DIFFRACTION99
3.12-3.360.33841490.23636042X-RAY DIFFRACTION98
3.36-3.70.25561310.21725904X-RAY DIFFRACTION95
3.7-4.240.26661220.19445243X-RAY DIFFRACTION85
4.24-5.330.21841200.18954879X-RAY DIFFRACTION79
5.34-43.060.23861210.17735190X-RAY DIFFRACTION83

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