PDB-4q6u: Crystal structure of a putative uncharacterized protein from Myco...

ID or keywords:

Entry

Database: PDB / ID: 4q6u

Title

Crystal structure of a putative uncharacterized protein from Mycobacterium tuberculosis

Components

Uncharacterized protein

Keywords

UNKNOWN FUNCTION / Seattle Structural Genoics for Infectious Disease / Mycobacterium tuberculosis / Structural Genomics / SSGCID / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Rv3651-like, middle domain / Rv3651-like, N-terminal / Rv3651-like, N-terminal / Rv3651-like, middle domain / cell wall / Uncharacterized protein / Uncharacterized protein

Function and homology information

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.95 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: Protein Sci. / Year: 2018
Title: Mycobacterium tuberculosis Rv3651 is a triple sensor-domain protein.
Authors: Abendroth, J. / Frando, A. / Phan, I.Q. / Staker, B.L. / Myler, P.J. / Edwards, T.E. / Grundner, C.

History

Deposition	Apr 23, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 18, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.2	Mar 7, 2018	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4q6u.cif.gz	266.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4q6u.ent.gz	223.3 KB	Display	PDB format
PDBx/mmJSON format	4q6u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4q6u_validation.pdf.gz	446.9 KB	Display	wwPDB validaton report
Full document	4q6u_full_validation.pdf.gz	451.5 KB	Display
Data in XML	4q6u_validation.xml.gz	28.6 KB	Display
Data in CIF	4q6u_validation.cif.gz	42.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q6/4q6u ftp://data.pdbj.org/pub/pdb/validation_reports/q6/4q6u	HTTPS FTP

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Related structure data

Similar structure data	6hq5-d 6hq7-d 5t7e-d 6r5d-d 3wmr-d 4dvz-d 6r5e-d 3zec-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: SSGCID-MytuD.18669.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

79 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	131.620, 73.020, 82.470
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-767- HOH

#1: Protein	Uncharacterized protein Mass: 39374.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: MT3753 / Plasmid: MytuD.18669.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O06357, UniProt: I6YCP0*PLUS
#2: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	2.53	51.4
2	2.53	51.4

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PACT screen, F2: 200mM NaBr, 100mM BisTris propane, 20% PEG 3350; MytuD.18669.a.B1 at 20.2mg/ml, cryo 15% EG; tray 252936 f2, puck iqo4-7, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 6.5

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	2

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	21-ID-F	1	0.97872
SYNCHROTRON	APS	21-ID-G	2	0.97856

Detector

Type	ID	Detector	Date
RAYONIX MX-225	1	CCD	Mar 6, 2014
RAYONIX MX-300	2	CCD	Mar 20, 2014

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Diamond [111]	SINGLE WAVELENGTH	M	x-ray	1
2	Diamond [111]	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97872	1
2	0.97856	1

Reflection

Number: 563190 / R_merge(I) obs: 0.062 / Χ²: 1.17 / D res high: 2.25 Å / Num. obs: 72498 / % possible obs: 99.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	Num. obs	ID	R_merge(I) obs
2.25	2.31	5381	1	0.508
2.31	2.37	5232	1	0.429
2.37	2.44	5049	1	0.369
2.44	2.52	4950	1	0.292
2.52	2.6	4789	1	0.241
2.6	2.69	4644	1	0.203
2.69	2.79	4450	1	0.159
2.79	2.9	4335	1	0.125
2.9	3.03	4106	1	0.102
3.03	3.18	3948	1	0.076
3.18	3.35	3728	1	0.06
3.35	3.56	3548	1	0.049
3.56	3.8	3340	1	0.042
3.8	4.11	3094	1	0.037
4.11	4.5	2854	1	0.033
4.5	5.03	2571	1	0.032
5.03	5.81	2283	1	0.033
5.81	7.12	1908	1	0.03
7.12	10.06	1484	1	0.024

Reflection

Resolution: 1.95→50 Å / Num. all: 58701 / Num. obs: 57563 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / B_iso Wilson estimate: 27.83 Å² / R_merge(I) obs: 0.065 / Net I/σ(I): 16.65

Reflection shell

Resolution: 1.95→2 Å / Redundancy: 6.2 % / R_merge(I) obs: 0.487 / Mean I/σ(I) obs: 3.36 / % possible all: 100

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	1.9_1692	refinement
PDB_EXTRACT	3.14	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.95→30.047 Å / SU ML: 0.21 / Isotropic thermal model: isotropic, TLS / σ(F): 1.36 / Phase error: 22.5 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2184	2824	4.91 %
R_work	0.1815	-	-
obs	0.1833	57529	98.05 %
all	-	58701	-

Solvent computation

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

Displacement parameters

B_iso mean: 42.913 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→30.047 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4860	0	16	443	5319

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5046
X-RAY DIFFRACTION	f_angle_d	1.04	6929
X-RAY DIFFRACTION	f_dihedral_angle_d	12.893	1822
X-RAY DIFFRACTION	f_chiral_restr	0.042	810
X-RAY DIFFRACTION	f_plane_restr	0.005	899

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 (%)
1.95-1.9836	0.3091	145	0.2393	2728	X-RAY DIFFRACTION	100
1.9836-2.0197	0.2657	152	0.2174	2750	X-RAY DIFFRACTION	100
2.0197-2.0585	0.2717	132	0.2106	2746	X-RAY DIFFRACTION	100
2.0585-2.1005	0.2848	134	0.2095	2763	X-RAY DIFFRACTION	100
2.1005-2.1462	0.2689	153	0.1983	2761	X-RAY DIFFRACTION	100
2.1462-2.1961	0.2546	135	0.1841	2761	X-RAY DIFFRACTION	100
2.1961-2.251	0.2205	137	0.1905	2752	X-RAY DIFFRACTION	100
2.251-2.3119	0.2276	133	0.1857	2754	X-RAY DIFFRACTION	100
2.3119-2.3799	0.2192	159	0.182	2733	X-RAY DIFFRACTION	100
2.3799-2.4566	0.248	148	0.1848	2753	X-RAY DIFFRACTION	99
2.4566-2.5444	0.2029	133	0.1849	2749	X-RAY DIFFRACTION	99
2.5444-2.6462	0.2071	142	0.1856	2741	X-RAY DIFFRACTION	99
2.6462-2.7666	0.2442	146	0.1908	2738	X-RAY DIFFRACTION	99
2.7666-2.9123	0.2259	135	0.1942	2748	X-RAY DIFFRACTION	98
2.9123-3.0946	0.2843	141	0.2007	2721	X-RAY DIFFRACTION	98
3.0946-3.3333	0.2083	144	0.1871	2752	X-RAY DIFFRACTION	97
3.3333-3.6682	0.215	149	0.1749	2705	X-RAY DIFFRACTION	96
3.6682-4.1977	0.1926	128	0.1571	2714	X-RAY DIFFRACTION	96
4.1977-5.284	0.1494	139	0.1484	2679	X-RAY DIFFRACTION	94
5.284-30.0505	0.2187	139	0.1884	2657	X-RAY DIFFRACTION	89

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	3.3214	0.0952	0.3226	0.6471	0.0622	1.4483	0.0159	-0.1438	-0.0491	-0	0.0013	0.1217	-0.0155	-0.2016	-0.0261	0.184	0.0054	-0.0005	0.0774	0.022	0.1703	53.7902	15.7583	28.2391
2	1.0223	0.1586	0.2446	1.4539	-0.005	0.1344	-0.0796	0.095	-0.0776	-0.0717	-0.0055	0.1413	-0.0964	0.0448	0.0941	0.2036	-0.0091	-0.0152	0.1136	0.0232	0.1659	67.7956	16.5695	23.697
3	3.9001	-0.0306	0.2992	1.6146	-0.2461	1.9016	0.1361	-0.9997	0.1069	0.3607	-0.0874	-0.1408	-0.0274	0.8511	-0.0447	0.3422	-0.0337	-0.0095	0.6154	0.0148	0.2726	89.7106	19.0036	29.2399
4	0.2129	-0.5353	-0.0803	2.5708	1.6789	2.321	0.1144	1.0344	-0.9621	-0.1383	-0.5657	0.9934	0.4257	-1.0032	0.2804	0.4061	-0.0143	-0.0867	1.1252	-0.3768	0.5928	62.6739	15.7355	-21.4414
5	3.1495	0.0258	1.7397	0.6271	0.131	2.4876	0.0996	0.7792	0.1012	-0.1694	-0.2491	0.2091	0.0905	-0.3708	0.1074	0.3111	0.0767	-0.0117	0.6811	-0.0419	0.2715	75.7607	21.9331	-18.332
6	3.7953	-0.544	-0.3656	4.5587	-0.5272	3.2603	0.0227	0.3575	-0.2726	-0.3189	-0.0055	0.2005	0.1507	-0.0938	-0.0273	0.2869	0.0309	-0.0087	0.4298	-0.1205	0.2337	78.3557	19.9663	-12.3545
7	1.0211	1.0321	0.8231	1.9051	-0.376	8.3334	0.0678	-0.02	0.1803	-0.031	-0.0012	-0.0468	-0.0467	0.3772	-0.0443	0.2458	-0.0267	0.0302	0.1816	0.0269	0.1836	86.5111	22.1109	4.336
8	2.2957	-0.5514	1.6788	1.8397	-0.9106	2.2555	0.2253	0.0672	-0.0765	0.1384	-0.2385	-0.0794	0.6299	0.8146	0.0673	0.3152	0.0474	0.0332	0.4883	0.0703	0.2578	100.7268	19.6571	-4.1711
9	2.1276	-1.2922	0.6633	1.5973	-0.1911	2.3421	-0.0035	-0.4687	-0.0641	-0.0339	-0.3541	-0.6026	0.3592	1.1673	0.2365	0.3437	0.0658	0.0198	0.7715	0.1074	0.3109	101.6578	17.5629	3.2098

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -5 through 163 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 164 through 227 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 228 through 339 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 53 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 54 through 163 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 164 through 207 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 208 through 248 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 249 through 287 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 288 through 338 )

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