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- PDB-8gll: R149E variant of Citrate Synthase (CitA) in Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 8gll
TitleR149E variant of Citrate Synthase (CitA) in Mycobacterium tuberculosis
Componentscitrate synthase
KeywordsCYTOSOLIC PROTEIN / Citrate Synthesis / TCA cycle / R149E 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
DI(HYDROXYETHYL)ETHER / Putative citrate synthase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsPathirage, R. / Ronning, D. / Petit, C.
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 22, 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
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)335,196109
Polymers327,9328
Non-polymers7,263101
Water10,467581
1
A: citrate synthase
B: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,51123
Polymers81,9832
Non-polymers1,52821
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12370 Å2
ΔGint-77 kcal/mol
Surface area28700 Å2
MethodPISA
2
C: citrate synthase
D: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,87642
Polymers81,9832
Non-polymers2,89340
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15610 Å2
ΔGint4 kcal/mol
Surface area28220 Å2
MethodPISA
3
E: citrate synthase
F: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,50123
Polymers81,9832
Non-polymers1,51721
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12220 Å2
ΔGint-102 kcal/mol
Surface area27950 Å2
MethodPISA
4
G: citrate synthase
H: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,30821
Polymers81,9832
Non-polymers1,32519
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11410 Å2
ΔGint-80 kcal/mol
Surface area28390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.933, 129.679, 270.153
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: 40991.523 Da / Num. of mol.: 8 / Mutation: R149E
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.: 75 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris pH 8.5, 0.2 M Lithium Sulfate, and 25 % PEG 3350

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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 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 100077 / % possible obs: 99.6 % / Redundancy: 10.6 % / CC1/2: 0.952 / CC star: 0.988 / Rmerge(I) obs: 0.249 / Rpim(I) all: 0.083 / Rrim(I) all: 0.264 / Χ2: 1.415 / Net I/σ(I): 4 / Num. measured all: 1056001
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.65-2.710.51.37249790.3310.7050.4661.4570.797100
2.7-2.7410.61.21849550.4880.810.4091.290.826100
2.74-2.810.61.11149700.4920.8120.3731.1770.83199.9
2.8-2.8510.50.99549900.5540.8450.3361.0550.853100
2.85-2.9210.60.91949290.5850.8590.3090.9740.884100
2.92-2.9810.60.81449550.6750.8980.2720.8630.91799.9
2.98-3.0610.60.66949930.7410.9230.2250.7090.96299.8
3.06-3.1410.50.59449830.7640.9310.1980.6291.00999.8
3.14-3.2310.60.51549420.8140.9470.1710.5451.02599.8
3.23-3.3410.60.4349890.8520.9590.1430.4551.08599.8
3.34-3.4610.60.34949790.9120.9770.1160.3691.16799.7
3.46-3.610.60.28549840.920.9790.0950.3011.25699.8
3.6-3.7610.60.24849830.9490.9870.0820.2621.35999.7
3.76-3.9610.60.20950060.9490.9870.0690.2211.68699.7
3.96-4.2110.60.18950110.9490.9870.0630.22.04299.4
4.21-4.5310.60.16450300.9720.9930.0540.1742.37799.5
4.53-4.9910.60.13650050.9820.9950.0450.1432.05399.2
4.99-5.7110.60.12250360.9860.9970.040.1291.54699.1
5.71-7.1910.50.10350960.9910.9980.0340.1091.6598.6
7.19-50100.07352620.9780.9940.0250.0783.94897.9

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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: 2.65→47.53 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2443 1999 2 %
Rwork0.19 --
obs0.1911 99930 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22176 0 452 581 23209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223031
X-RAY DIFFRACTIONf_angle_d0.42731187
X-RAY DIFFRACTIONf_dihedral_angle_d4.363358
X-RAY DIFFRACTIONf_chiral_restr0.0373415
X-RAY DIFFRACTIONf_plane_restr0.0044117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.720.37521010.26784935X-RAY DIFFRACTION70
2.72-2.790.30681440.24737089X-RAY DIFFRACTION100
2.79-2.870.32891460.24567134X-RAY DIFFRACTION100
2.87-2.960.2981440.23977064X-RAY DIFFRACTION100
2.96-3.070.3371450.24647092X-RAY DIFFRACTION100
3.07-3.190.30871460.24967109X-RAY DIFFRACTION100
3.19-3.340.30911450.23047150X-RAY DIFFRACTION100
3.34-3.510.28341450.20727092X-RAY DIFFRACTION100
3.51-3.730.2791460.19327143X-RAY DIFFRACTION100
3.73-4.020.23511460.17067144X-RAY DIFFRACTION100
4.02-4.430.1951460.15567180X-RAY DIFFRACTION100
4.43-5.070.19021460.14717172X-RAY DIFFRACTION99
5.07-6.380.19561480.17297226X-RAY DIFFRACTION99
6.38-47.530.18341510.15737401X-RAY DIFFRACTION98

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