PDB-8glb: Selenomethionine Derivatized Citrate Synthase (CitA) in Mycobacte...

ID or keywords:

Entry

Database: PDB / ID: 8glb

Title

Selenomethionine Derivatized Citrate Synthase (CitA) in Mycobacterium tuberculosis with Pyruvate

Components

citrate synthase

Keywords

CYTOSOLIC PROTEIN / Citrate Synthesis / TCA cycle / Pyruvate

Function / homology

Function and homology information

citrate synthase (unknown stereospecificity) / : / tricarboxylic acid cycle / carbohydrate metabolic process / cytosol
Similarity search - Function

Biological species

Mycobacterium tuberculosis H37Rv (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.1 Å

Authors

Pathirage, R. / Ronning, D. / Favrot, L.

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 21, 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
Revision 2.0	Nov 15, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8glb.cif.gz	306.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8glb.ent.gz	247.6 KB	Display	PDB format
PDBx/mmJSON format	8glb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8glb_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	8glb_full_validation.pdf.gz	1.5 MB	Display
Data in XML	8glb_validation.xml.gz	60.6 KB	Display
Data in CIF	8glb_validation.cif.gz	88.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gl/8glb ftp://data.pdbj.org/pub/pdb/validation_reports/gl/8glb	HTTPS FTP

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Related structure data

Related structure data	8gi7C 8giwC 8gllC 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) #102 - Jun 2008 Lactate Dehydrogenase similarity (1) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1)

Deposited unit

A: citrate synthase

B: citrate synthase

C: citrate synthase

D: citrate synthase

hetero molecules

165 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: citrate synthase

D: citrate synthase

hetero molecules

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

2

B: citrate synthase

C: citrate synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	75.856, 130.127, 92.484
Angle α, β, γ (deg.)	90.00, 107.09, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#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.: 13 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-PYR / PYRUVIC ACID Mass: 88.062 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₄O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 972 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.66 Å³/Da / Density % sol: 53.74 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris pH 8.5, 0.5 M sodium chloride, 19 % w/v polyethylene glycol, 5.6 micromolar CYMAL-6

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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: Oct 17, 2013

Radiation

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

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 2.1→50 Å / Num. obs: 97981 / % possible obs: 99.3 % / Redundancy: 5.6 % / CC_1/2: 0.966 / CC star: 0.991 / R_merge(I) obs: 0.229 / R_pim(I) all: 0.108 / R_rim(I) all: 0.254 / Χ²: 1.708 / Net I/σ(I): 3.3

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
2.1-2.14	5.8	1.966	4895	0.316	0.693	0.901	2.167	0.682	100
2.14-2.18	5.8	1.678	4918	0.408	0.762	0.77	1.849	0.702	100
2.18-2.22	5.8	1.39	4915	0.47	0.8	0.638	1.533	0.707	100
2.22-2.26	5.2	1.145	4885	0.147	0.507	0.577	1.288	1.373	99.6
2.26-2.31	5.8	0.992	4941	0.65	0.888	0.456	1.093	0.739	100
2.31-2.37	5.8	0.849	4923	0.734	0.92	0.389	0.935	0.738	100
2.37-2.42	5.8	0.704	4911	0.773	0.934	0.322	0.776	0.765	100
2.42-2.49	5.8	0.596	4915	0.809	0.946	0.273	0.657	0.793	100
2.49-2.56	5.8	0.568	4924	0.845	0.957	0.253	0.623	0.856	100
2.56-2.65	5.8	0.442	4953	0.881	0.968	0.202	0.487	0.884	100
2.65-2.74	5.8	0.347	4859	0.917	0.978	0.159	0.382	0.979	100
2.74-2.85	5.8	0.29	4954	0.944	0.985	0.133	0.32	1.006	100
2.85-2.98	5.8	0.255	4923	0.955	0.988	0.117	0.281	1.081	100
2.98-3.14	5.8	0.208	4937	0.967	0.992	0.096	0.23	1.222	99.9
3.14-3.33	5.8	0.176	4932	0.968	0.992	0.081	0.194	1.375	100
3.33-3.59	5.6	0.149	4938	0.968	0.992	0.07	0.165	2.126	99.8
3.59-3.95	5.1	0.141	4890	0.937	0.984	0.071	0.158	2.881	99
3.95-4.52	5.1	0.1	4810	0.978	0.994	0.051	0.112	2.919	97.1
4.52-5.7	5	0.088	4791	0.982	0.995	0.045	0.1	3.156	96.3
5.7-50	5	0.11	4796	0.972	0.993	0.054	0.123	11.44	95.1

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Processing

Software

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

Refinement

Method to determine structure:

SAD / Resolution: 2.1→49.4 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.241	3918	2.04 %
R_work	0.1877	-	-
obs	0.1887	97981	98.25 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→49.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11170	0	76	972	12218

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	11511
X-RAY DIFFRACTION	f_angle_d	0.65	15650
X-RAY DIFFRACTION	f_dihedral_angle_d	5.909	1658
X-RAY DIFFRACTION	f_chiral_restr	0.041	1723
X-RAY DIFFRACTION	f_plane_restr	0.006	2086

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 (%)
2.1-2.13	0.3523	114	0.319	5740	X-RAY DIFFRACTION	85
2.13-2.16	0.3368	145	0.3068	6857	X-RAY DIFFRACTION	99
2.16-2.19	0.4104	142	0.3019	6868	X-RAY DIFFRACTION	100
2.19-2.22	0.3039	141	0.2879	6867	X-RAY DIFFRACTION	100
2.22-2.25	0.3608	141	0.2901	6817	X-RAY DIFFRACTION	100
2.25-2.28	0.3484	143	0.2865	6796	X-RAY DIFFRACTION	99
2.28-2.32	0.2981	140	0.2589	6855	X-RAY DIFFRACTION	100
2.32-2.35	0.271	143	0.2513	6869	X-RAY DIFFRACTION	100
2.35-2.4	0.3028	140	0.2411	6757	X-RAY DIFFRACTION	100
2.4-2.44	0.289	140	0.2276	6886	X-RAY DIFFRACTION	100
2.44-2.49	0.2793	144	0.2232	6831	X-RAY DIFFRACTION	100
2.49-2.54	0.2652	145	0.2172	6921	X-RAY DIFFRACTION	100
2.54-2.59	0.2737	142	0.2151	6798	X-RAY DIFFRACTION	100
2.59-2.65	0.2542	146	0.2067	6896	X-RAY DIFFRACTION	100
2.65-2.72	0.2448	145	0.1975	6873	X-RAY DIFFRACTION	100
2.72-2.79	0.2567	142	0.1859	6890	X-RAY DIFFRACTION	100
2.79-2.87	0.236	143	0.1883	6762	X-RAY DIFFRACTION	100
2.87-2.97	0.2602	141	0.1872	6874	X-RAY DIFFRACTION	100
2.97-3.07	0.2413	142	0.1918	6866	X-RAY DIFFRACTION	100
3.07-3.2	0.2048	142	0.1777	6822	X-RAY DIFFRACTION	100
3.2-3.34	0.2656	141	0.177	6841	X-RAY DIFFRACTION	100
3.34-3.52	0.2652	144	0.166	6805	X-RAY DIFFRACTION	100
3.52-3.74	0.22	143	0.1632	6824	X-RAY DIFFRACTION	99
3.74-4.03	0.1913	138	0.1443	6678	X-RAY DIFFRACTION	97
4.03-4.43	0.1997	137	0.137	6530	X-RAY DIFFRACTION	95
4.43-5.07	0.1745	131	0.1427	6319	X-RAY DIFFRACTION	92
5.07-6.39	0.2214	135	0.1673	6527	X-RAY DIFFRACTION	96
6.39-49.4	0.1949	128	0.1645	6178	X-RAY DIFFRACTION	90

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