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

ID or keywords:

Entry

Database: PDB / ID: 8gll

Title

R149E variant of Citrate Synthase (CitA) in Mycobacterium tuberculosis

Components

citrate synthase

Keywords

CYTOSOLIC PROTEIN / Citrate Synthesis / TCA cycle / R149E variant

Function / homology

Function and homology information

citrate synthase (unknown stereospecificity) /

citrate synthase activity /

tricarboxylic acid cycle
Similarity search - Function

Biological species

Mycobacterium tuberculosis H37Rv (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Pathirage, R. / Ronning, D. / Petit, C.

Funding support

United States, 1items

Citation

Journal: 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

Deposition	Mar 22, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 7, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8gll.cif.gz	562.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8gll.ent.gz	467.9 KB	Display	PDB format
PDBx/mmJSON format	8gll.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gl/8gll ftp://data.pdbj.org/pub/pdb/validation_reports/gl/8gll	HTTPS FTP

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Related structure data

Related structure data	8gi7C 8giwC 8glbC 8gm9C 8gmfC 8gmiC 8gmkC 8s97C 8s9dC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#93 - Sep 2007 Citrate Synthase similarity (8) #154 - Oct 2012 Citric Acid Cycle similarity (7)

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

335 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: citrate synthase

B: citrate synthase

hetero molecules

defined by author&software
Evidence: gel filtration
83.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: citrate synthase

D: citrate synthase

hetero molecules

defined by author&software
84.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: citrate synthase

F: citrate synthase

hetero molecules

defined by author&software
83.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: citrate synthase

H: citrate synthase

hetero molecules

defined by author&software
83.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	19
Space group name H-M	P2₁2₁2₁

#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 / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 75 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 581 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.67 Å³/Da / Density % sol: 53.93 %
Crystal grow	Temperature: 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

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Aug 17, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 2.65→50 Å / Num. obs: 100077 / % possible obs: 99.6 % / Redundancy: 10.6 % / CC_1/2: 0.952 / CC star: 0.988 / R_merge(I) obs: 0.249 / R_pim(I) all: 0.083 / R_rim(I) all: 0.264 / Χ²: 1.415 / Net I/σ(I): 4 / Num. measured all: 1056001

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.65-2.7	10.5	1.372	4979	0.331	0.705	0.466	1.457	0.797	100
2.7-2.74	10.6	1.218	4955	0.488	0.81	0.409	1.29	0.826	100
2.74-2.8	10.6	1.111	4970	0.492	0.812	0.373	1.177	0.831	99.9
2.8-2.85	10.5	0.995	4990	0.554	0.845	0.336	1.055	0.853	100
2.85-2.92	10.6	0.919	4929	0.585	0.859	0.309	0.974	0.884	100
2.92-2.98	10.6	0.814	4955	0.675	0.898	0.272	0.863	0.917	99.9
2.98-3.06	10.6	0.669	4993	0.741	0.923	0.225	0.709	0.962	99.8
3.06-3.14	10.5	0.594	4983	0.764	0.931	0.198	0.629	1.009	99.8
3.14-3.23	10.6	0.515	4942	0.814	0.947	0.171	0.545	1.025	99.8
3.23-3.34	10.6	0.43	4989	0.852	0.959	0.143	0.455	1.085	99.8
3.34-3.46	10.6	0.349	4979	0.912	0.977	0.116	0.369	1.167	99.7
3.46-3.6	10.6	0.285	4984	0.92	0.979	0.095	0.301	1.256	99.8
3.6-3.76	10.6	0.248	4983	0.949	0.987	0.082	0.262	1.359	99.7
3.76-3.96	10.6	0.209	5006	0.949	0.987	0.069	0.221	1.686	99.7
3.96-4.21	10.6	0.189	5011	0.949	0.987	0.063	0.2	2.042	99.4
4.21-4.53	10.6	0.164	5030	0.972	0.993	0.054	0.174	2.377	99.5
4.53-4.99	10.6	0.136	5005	0.982	0.995	0.045	0.143	2.053	99.2
4.99-5.71	10.6	0.122	5036	0.986	0.997	0.04	0.129	1.546	99.1
5.71-7.19	10.5	0.103	5096	0.991	0.998	0.034	0.109	1.65	98.6
7.19-50	10	0.073	5262	0.978	0.994	0.025	0.078	3.948	97.9

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158:000	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHENIX		phasing

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.2443	1999	2 %
R_work	0.19	-	-
obs	0.1911	99930	97.4 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.65→47.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22176	0	452	581	23209

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	23031
X-RAY DIFFRACTION	f_angle_d	0.427	31187
X-RAY DIFFRACTION	f_dihedral_angle_d	4.36	3358
X-RAY DIFFRACTION	f_chiral_restr	0.037	3415
X-RAY DIFFRACTION	f_plane_restr	0.004	4117

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.65-2.72	0.3752	101	0.2678	4935	X-RAY DIFFRACTION	70
2.72-2.79	0.3068	144	0.2473	7089	X-RAY DIFFRACTION	100
2.79-2.87	0.3289	146	0.2456	7134	X-RAY DIFFRACTION	100
2.87-2.96	0.298	144	0.2397	7064	X-RAY DIFFRACTION	100
2.96-3.07	0.337	145	0.2464	7092	X-RAY DIFFRACTION	100
3.07-3.19	0.3087	146	0.2496	7109	X-RAY DIFFRACTION	100
3.19-3.34	0.3091	145	0.2304	7150	X-RAY DIFFRACTION	100
3.34-3.51	0.2834	145	0.2072	7092	X-RAY DIFFRACTION	100
3.51-3.73	0.279	146	0.1932	7143	X-RAY DIFFRACTION	100
3.73-4.02	0.2351	146	0.1706	7144	X-RAY DIFFRACTION	100
4.02-4.43	0.195	146	0.1556	7180	X-RAY DIFFRACTION	100
4.43-5.07	0.1902	146	0.1471	7172	X-RAY DIFFRACTION	99
5.07-6.38	0.1956	148	0.1729	7226	X-RAY DIFFRACTION	99
6.38-47.53	0.1834	151	0.1573	7401	X-RAY DIFFRACTION	98

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