PDB-9f80: Crystal structure of Rv2242 regulator C-terminal fragment (161-414)

ID or keywords:

Entry

Database: PDB / ID: 9f80

Title

Crystal structure of Rv2242 regulator C-terminal fragment (161-414)

Components

Uncharacterized protein Rv2242

Keywords

TRANSCRIPTION / HELIX-TURN-HELIX / PUCR FAMILY / TUBERCULOSIS / DNA BINDING PROTEIN

Function / homology

PucR C-terminal helix-turn-helix domain / PucR C-terminal helix-turn-helix domain superfamily / : / PucR C-terminal helix-turn-helix domain / CdaR, GGDEF-like domain / GGDEF-like domain / Uncharacterized protein Rv2242

Function and homology information

Biological species

Mycobacterium tuberculosis H37Rv (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.027 Å

Authors

Megalizzi, V. / Tanina, A. / Grosse, C. / Mirgaux, M. / Legrand, P. / Dias Mirandela, G. / Wohlkonig, A. / Bifani, P. / Wintjens, R.

Funding support

Belgium, 1items

Citation

Journal: Heliyon / Year: 2024
Title: Domain architecture of the Mycobacterium tuberculosis MabR ( Rv2242 ), a member of the PucR transcription factor family.
Authors: Megalizzi, V. / Tanina, A. / Grosse, C. / Mirgaux, M. / Legrand, P. / Dias Mirandela, G. / Wohlkonig, A. / Bifani, P. / Wintjens, R.

History

Deposition	May 6, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 18, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9f80.cif.gz	65.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9f80.ent.gz	43.4 KB	Display	PDB format
PDBx/mmJSON format	9f80.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/f8/9f80 ftp://data.pdbj.org/pub/pdb/validation_reports/f8/9f80	HTTPS FTP

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Related structure data

Related structure data	9fb1C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein Rv2242

hetero molecules

29.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	63.040, 75.280, 139.520
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-624- HOH

#1: Protein	Uncharacterized protein Rv2242 Mass: 29106.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: Rv2242, MTCY427.23 / Plasmid: plasmid / Details (production host): pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WPH5
#2: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	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: 2.85 Å³/Da / Density % sol: 56.88 %
Crystal grow	Temperature: 277 K / Method: slow cooling / pH: 7.5 Details: 20 mM HEPES, pH7.5, 400 mM NaCl, 5% glycerol, 5 mM beta-mercaptoethanol, 400 mM imidazole, temperature 277K, slow cooling

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.027→48.378 Å / Num. obs: 21908 / % possible obs: 99.7 % / Redundancy: 13.4 % / CC_1/2: 0.732 / R_rim(I) all: 0.073 / Net I/σ(I): 22.81
Reflection shell	Resolution: 2.027→2.15 Å / Redundancy: 13.5 % / Num. unique obs: 3440 / CC_1/2: 0.681 / R_rim(I) all: 1.353 / % possible all: 98.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0405	refinement
XDS	20190315	data reduction
XDS	20190315	data scaling
SHELXD	2016/1	phasing
PHASER	2.8.3	phasing
MOLREP	11.7.02	phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.027→48.378 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.945 / SU B: 4.703 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.156
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2543	1096	5.003 %
R_work	0.1964	20812	-
all	0.199	-	-
obs	-	21908	99.754 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 51.793 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.995 Å²	-0 Å²	0 Å²
2-	-	-0.834 Å²	-0 Å²
3-	-	-	-1.161 Å²

Refinement step

Cycle: LAST / Resolution: 2.027→48.378 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1787	0	9	38	1834

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.012	1829
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1754
X-RAY DIFFRACTION	r_angle_refined_deg	2.207	1.653	2501
X-RAY DIFFRACTION	r_angle_other_deg	0.703	1.577	4017
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.114	5	241
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	15.777	5	19
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.098	10	268
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.123	10	70
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	297
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	2212
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	400
X-RAY DIFFRACTION	r_nbd_refined	0.244	0.2	435
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.205	0.2	1601
X-RAY DIFFRACTION	r_nbtor_refined	0.195	0.2	934
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.088	0.2	1034
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.177	0.2	66
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.12	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.211	0.2	67
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.134	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	6.459	5.09	971
X-RAY DIFFRACTION	r_mcbond_other	6.448	5.09	970
X-RAY DIFFRACTION	r_mcangle_it	8.033	9.079	1209
X-RAY DIFFRACTION	r_mcangle_other	8.045	9.084	1210
X-RAY DIFFRACTION	r_scbond_it	7.976	5.632	858
X-RAY DIFFRACTION	r_scbond_other	7.972	5.636	859
X-RAY DIFFRACTION	r_scangle_it	10.5	10.031	1292
X-RAY DIFFRACTION	r_scangle_other	10.496	10.03	1293
X-RAY DIFFRACTION	r_lrange_it	11.606	49.81	2048
X-RAY DIFFRACTION	r_lrange_other	11.657	49.819	2047

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.027-2.079	0.484	77	0.389	1453	0.394	1581	0.861	0.913	96.7742	0.386
2.079-2.136	0.315	79	0.302	1509	0.303	1588	0.912	0.945	100	0.292
2.136-2.198	0.319	74	0.279	1409	0.281	1483	0.949	0.951	100	0.261
2.198-2.265	0.327	74	0.29	1411	0.292	1486	0.922	0.948	99.9327	0.265
2.265-2.339	0.281	73	0.222	1376	0.225	1449	0.956	0.97	100	0.195
2.339-2.421	0.239	68	0.203	1298	0.205	1366	0.965	0.976	100	0.178
2.421-2.513	0.25	67	0.207	1272	0.209	1339	0.957	0.974	100	0.177
2.513-2.615	0.333	65	0.221	1222	0.226	1287	0.928	0.97	100	0.193
2.615-2.731	0.31	62	0.209	1197	0.214	1259	0.938	0.975	100	0.183
2.731-2.864	0.294	59	0.197	1114	0.202	1173	0.939	0.978	100	0.175
2.864-3.018	0.264	57	0.215	1076	0.218	1133	0.963	0.974	100	0.191
3.018-3.2	0.279	53	0.193	1016	0.197	1069	0.957	0.978	100	0.176
3.2-3.42	0.26	51	0.204	961	0.206	1012	0.961	0.976	100	0.193
3.42-3.693	0.274	47	0.216	903	0.219	950	0.963	0.976	100	0.209
3.693-4.043	0.232	44	0.191	839	0.193	883	0.97	0.979	100	0.189
4.043-4.516	0.238	41	0.156	762	0.159	803	0.976	0.986	100	0.164
4.516-5.207	0.239	34	0.159	663	0.162	697	0.973	0.987	100	0.174
5.207-6.359	0.209	32	0.198	591	0.199	623	0.978	0.981	100	0.205
6.359-8.916	0.201	23	0.144	450	0.146	473	0.976	0.989	100	0.162
8.916-48.378	0.133	16	0.156	290	0.155	307	0.986	0.982	99.6743	0.191

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