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- PDB-8x0a: Crystal Structure of MftR from mycobacterium tuberculosis -

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Open data

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Basic information

Entry

Database: PDB / ID: 8x0a

Title

Crystal Structure of MftR from mycobacterium tuberculosis

Components

Putative mycofactocin biosynthesis transcriptional regulator MftR

Keywords

DNA BINDING PROTEIN / transcriptional factor

Function / homology

Function and homology information

transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Peng, F. / Ke, Z.H. / Li, Y.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of MftR from mycobacterium tuberculosis
Authors: Peng, F. / Ke, Z.H. / Li, Y.

History

Deposition	Nov 4, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 6, 2024	Provider: repository / Type: Initial release

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	8x0a.cif.gz	185.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8x0a.ent.gz	150.1 KB	Display	PDB format
PDBx/mmJSON format	8x0a.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8x0a_validation.pdf.gz	463.8 KB	Display	wwPDB validaton report
Full document	8x0a_full_validation.pdf.gz	479.8 KB	Display
Data in XML	8x0a_validation.xml.gz	37.4 KB	Display
Data in CIF	8x0a_validation.cif.gz	49.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x0/8x0a ftp://data.pdbj.org/pub/pdb/validation_reports/x0/8x0a	HTTPS FTP

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Related structure data

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

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Assembly

Deposited unit

A: Putative mycofactocin biosynthesis transcriptional regulator MftR

E: Putative mycofactocin biosynthesis transcriptional regulator MftR

B: Putative mycofactocin biosynthesis transcriptional regulator MftR

C: Putative mycofactocin biosynthesis transcriptional regulator MftR

D: Putative mycofactocin biosynthesis transcriptional regulator MftR

104 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative mycofactocin biosynthesis transcriptional regulator MftR

E: Putative mycofactocin biosynthesis transcriptional regulator MftR

B: Putative mycofactocin biosynthesis transcriptional regulator MftR

C: Putative mycofactocin biosynthesis transcriptional regulator MftR

D: Putative mycofactocin biosynthesis transcriptional regulator MftR

A: Putative mycofactocin biosynthesis transcriptional regulator MftR

E: Putative mycofactocin biosynthesis transcriptional regulator MftR

B: Putative mycofactocin biosynthesis transcriptional regulator MftR

C: Putative mycofactocin biosynthesis transcriptional regulator MftR

D: Putative mycofactocin biosynthesis transcriptional regulator MftR

defined by author&software
Evidence: gel filtration, homology
208 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	109.750, 81.430, 120.457
Angle α, β, γ (deg.)	90.000, 107.356, 90.000
Int Tables number	5
Space group name H-M	I121

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Components

#1: Protein	Putative mycofactocin biosynthesis transcriptional regulator MftR Mass: 20840.643 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mftR / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P9WMB7
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experimental details

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.1 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl, and 2 M (NH4)2SO4

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97902 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2022
Radiation	Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97902 Å / Relative weight: 1
Reflection	Resolution: 2.7→47.38 Å / Num. obs: 27862 / % possible obs: 95.7 % / Redundancy: 3.8 % / CC_1/2: 0.996 / Net I/σ(I): 10.9
Reflection shell	Resolution: 2.7→2.83 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3691 / CC_1/2: 0.688

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0350	refinement
XDS		data reduction
Aimless		data scaling
PHASES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.7→47.38 Å / Cor.coef. F_o:F_c: 0.928 / Cor.coef. F_o:F_c free: 0.888 / Cross valid method: THROUGHOUT / ESU R Free: 0.402
Details: Hydrogens have been used if present in the input file

	R_factor	Num. reflection	% reflection
R_free	0.2783	1380	4.953 %
R_work	0.2291	26481	-
all	0.231	-	-
obs	-	27861	99.376 %

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: 48.104 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.289 Å²	0 Å²	0.47 Å²
2-	-	1.699 Å²	-0 Å²
3-	-	-	-1.425 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→47.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7237	0	0	51	7288

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	7392
X-RAY DIFFRACTION	r_angle_refined_deg	1.899	1.632	10027
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.333	5	913
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	17.562	10	79
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.408	10	1200
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.213	10	349
X-RAY DIFFRACTION	r_chiral_restr	0.11	0.2	1133
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	5543
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	3105
X-RAY DIFFRACTION	r_nbtor_refined	0.293	0.2	5105
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.177	0.2	169
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.357	0.2	141
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.921	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	5.006	4.572	3667
X-RAY DIFFRACTION	r_mcangle_it	7.504	6.853	4575
X-RAY DIFFRACTION	r_scbond_it	5.319	4.99	3725
X-RAY DIFFRACTION	r_scangle_it	7.814	7.331	5452
X-RAY DIFFRACTION	r_lrange_it	11.291	75.325	10997

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
2.7-2.77	0.406	101	0.317	1948	0.321	2060	0.889	0.936	99.466	0.295
2.77-2.846	0.33	90	0.297	1922	0.298	2018	0.927	0.945	99.7027	0.271
2.846-2.928	0.336	93	0.301	1834	0.303	1932	0.926	0.945	99.7412	0.271
2.928-3.018	0.337	90	0.283	1807	0.286	1901	0.923	0.95	99.7896	0.255
3.018-3.116	0.362	98	0.253	1723	0.259	1826	0.932	0.958	99.7262	0.222
3.116-3.225	0.303	83	0.268	1669	0.27	1755	0.933	0.957	99.8291	0.24
3.225-3.346	0.276	88	0.252	1640	0.253	1736	0.954	0.959	99.5392	0.233
3.346-3.482	0.363	76	0.237	1567	0.243	1652	0.912	0.965	99.4552	0.216
3.482-3.636	0.268	79	0.23	1498	0.232	1581	0.959	0.968	99.747	0.209
3.636-3.812	0.274	76	0.219	1431	0.222	1511	0.95	0.972	99.7353	0.204
3.812-4.017	0.27	76	0.208	1386	0.211	1463	0.945	0.973	99.9316	0.198
4.017-4.259	0.256	89	0.207	1267	0.21	1364	0.959	0.974	99.4135	0.2
4.259-4.55	0.213	65	0.195	1216	0.196	1288	0.972	0.977	99.4565	0.193
4.55-4.911	0.228	49	0.198	1138	0.2	1193	0.96	0.976	99.4971	0.196
4.911-5.374	0.295	56	0.21	1052	0.214	1119	0.954	0.974	99.017	0.206
5.374-5.999	0.234	47	0.243	948	0.242	1000	0.967	0.965	99.5	0.239
5.999-6.908	0.325	43	0.241	849	0.245	895	0.951	0.965	99.6648	0.243
6.908-8.416	0.229	36	0.195	726	0.196	769	0.968	0.978	99.0897	0.217
8.416-11.719	0.213	33	0.17	558	0.173	605	0.977	0.981	97.686	0.202
11.719-47.38	0.308	12	0.231	302	0.234	362	0.957	0.965	86.7403	0.261

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