PDB-4x2m: Structure of Mtr2

ID or keywords:

Entry

Database: PDB / ID: 4x2m

Title

Structure of Mtr2

Components

Mtr2

Keywords

TRANSPORT PROTEIN / mRNA nuclear export factor

Function / homology

Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / NTF2-like domain superfamily / NTF2 domain-containing protein

Function and homology information

Biological species

Chaetomium thermophilum (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2 Å

Authors

Aibara, S. / Valkov, E. / Stewart, M.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structural characterization of the principal mRNA-export factor Mex67-Mtr2 from Chaetomium thermophilum.
Authors: Aibara, S. / Valkov, E. / Lamers, M.H. / Dimitrova, L. / Hurt, E. / Stewart, M.

History

Deposition	Nov 26, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jul 15, 2015	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4x2m.cif.gz	214.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4x2m.ent.gz	185.2 KB	Display	PDB format
PDBx/mmJSON format	4x2m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4x2m_validation.pdf.gz	418.6 KB	Display	wwPDB validaton report
Full document	4x2m_full_validation.pdf.gz	419.6 KB	Display
Data in XML	4x2m_validation.xml.gz	17.7 KB	Display
Data in CIF	4x2m_validation.cif.gz	25.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x2/4x2m ftp://data.pdbj.org/pub/pdb/validation_reports/x2/4x2m	HTTPS FTP

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Related structure data

Related structure data	4wp2C 4wp5C 4wp6C 4wpmC 4xm4C C: citing same article (ref.)
Similar structure data	6zpr-d 2v9s-1 5hb5-2 4lpj-d 2ygv-2 1vei-d 3szm-1 3f33-d 2v9s-4 6h1x-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#44 - Aug 2003 Calmodulin similarity (1)

Deposited unit

A: Mtr2

B: Mtr2

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

1

A: Mtr2

defined by author&software
20.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Mtr2

defined by author&software
20.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	83.958, 83.958, 131.340
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Mtr2 Mass: 20909.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0065500 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SG92
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.77 Å³/Da / Density % sol: 55.55 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 1.26 M Ammonium Sulphate, 0.1 M MES pH 6.0. See publication for details.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9686 Å / Relative weight: 1
Reflection	Resolution: 2→38.8266 Å / Num. obs: 31939 / % possible obs: 98.7 % / Redundancy: 4.3 % / Net I/σ(I): 12.2

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Resolution: 2→38.819 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2018	1612	5.06 %
R_work	0.1807	-	-
obs	0.1818	31871	98.24 %

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→38.819 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2863	0	0	332	3195

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	2940
X-RAY DIFFRACTION	f_angle_d	0.716	3992
X-RAY DIFFRACTION	f_dihedral_angle_d	11.154	1079
X-RAY DIFFRACTION	f_chiral_restr	0.029	422
X-RAY DIFFRACTION	f_plane_restr	0.003	519

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 (%)
2-2.0589	0.2807	141	0.2633	2493	X-RAY DIFFRACTION	100
2.0589-2.1253	0.2671	119	0.2416	2506	X-RAY DIFFRACTION	100
2.1253-2.2013	0.3002	143	0.2273	2507	X-RAY DIFFRACTION	100
2.2013-2.2894	0.2655	121	0.2164	2543	X-RAY DIFFRACTION	99
2.2894-2.3936	0.2549	127	0.208	2503	X-RAY DIFFRACTION	99
2.3936-2.5198	0.2305	126	0.1975	2519	X-RAY DIFFRACTION	99
2.5198-2.6776	0.2008	131	0.1841	2540	X-RAY DIFFRACTION	100
2.6776-2.8843	0.1978	144	0.1934	2538	X-RAY DIFFRACTION	99
2.8843-3.1744	0.2209	145	0.1805	2510	X-RAY DIFFRACTION	99
3.1744-3.6335	0.2124	141	0.1696	2526	X-RAY DIFFRACTION	98
3.6335-4.5767	0.1429	140	0.1433	2500	X-RAY DIFFRACTION	95
4.5767-38.8266	0.1719	134	0.1655	2574	X-RAY DIFFRACTION	93

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	0.3498	-0.1054	0.0637	0.1697	-0.0079	0.0185	-0.01	-0.055	-0.0324	0.0327	0.0395	-0.0639	0.0099	-0.0258	0	0.1511	-0.0226	-0.0092	0.1872	0.0003	0.1619	96.6518	52.022	62.6071
2	-0.0147	-0.0181	0.0024	0.0387	0.0417	0.1408	0.2206	-0.0858	0.1814	0.0201	0.003	-0.0361	-0.1967	0.0133	-0	0.1741	-0.024	0.0095	0.186	-0.018	0.2141	90.0897	65.6255	65.3824
3	0.2194	0.1792	0.2321	0.213	-0.0848	0.161	-0.0141	0.0142	0.0557	0.096	0.0913	0.0102	0.0135	-0.2201	0	0.1765	0.0099	0.0211	0.207	0.0156	0.1872	78.6463	56.6059	68.4174
4	0.0725	0.0087	-0.0686	0.0067	-0.0006	0.0665	0.194	-0.0202	-0.2567	0.1616	-0.0632	-0.0871	0.2178	0.1887	0	0.2677	0.018	-0.0395	0.2206	-0.0334	0.2642	108.0098	41.5962	52.647
5	0.0568	0.0599	0.0246	0.1425	0.0495	0.0824	-0.0398	0.0377	-0.0202	0.0762	0.0106	0.0059	0.1757	-0.1525	-0	0.1553	-0.0124	0.006	0.2441	-0.0209	0.1606	77.2898	54.0534	64.7516
6	0.1777	0.162	-0.0664	0.1223	0.1219	0.174	0.0626	-0.026	-0.1161	-0.0908	0.0255	0.0376	0.0345	-0.0277	0	0.1373	-0.0141	-0.0167	0.1532	0.0009	0.1542	93.6817	52.4471	59.1245
7	0.1665	0.134	-0.0065	0.0387	-0.0582	0.0528	0.0209	0.0219	-0.0119	-0.0884	-0.0954	-0.1903	0.0998	0.0959	-0	0.1936	0.0057	-0.004	0.1865	0.0048	0.1793	76.8311	38.5718	45.2711
8	0.1428	-0.0537	0.1083	0.0737	-0.1514	0.0924	0.062	-0.0216	-0.0631	-0.1448	0.0569	0.1268	0.0132	-0.1636	-0	0.1921	-0.0411	-0.0265	0.2069	0.0191	0.1789	61.4731	35.8723	45.6893
9	0.0092	-0.0922	0.0404	0.0264	-0.0922	0.0789	0.0053	0.0079	0.0559	-0.0132	0.0985	0.0912	-0.0289	-0.147	0	0.1454	-0.0091	-0.0144	0.1915	0.0035	0.2024	60.8336	50.1471	42.7213
10	-0.0225	0.0304	0.197	0.0618	-0.029	-0.0527	0.0016	-0.0488	0.0136	0.0605	0.009	-0.0704	-0.1305	-0.0625	0	0.171	0.0233	0.0074	0.1978	0.0116	0.1863	74.7749	54.5966	39.7001
11	0.0116	-0.0001	-0.0116	0.003	-0.0211	0.0281	0.0189	0.0749	-0.2341	0.0946	0.1343	-0.1061	0.263	-0.017	-0	0.2429	-0.016	-0.003	0.1518	0.0275	0.2326	67.1642	24.738	57.1444
12	0.2033	0.076	-0.071	0.1618	-0.0099	0.4624	-0.0587	-0.0039	-0.0048	0.0662	0.0779	-0.1398	0.0723	-0.0549	0	0.1435	-0.0093	-0.0037	0.1632	-0.0057	0.1505	74.4255	41.0749	48.9402
13	0.0037	-0.0345	-0.0209	0.0278	0.0167	0.0074	0.2292	0.1777	-0.0363	-0.6211	-0.0504	-0.0776	0.124	0.3208	0	0.405	0.0003	0.0052	0.228	0.0113	0.1823	70.2487	24.8516	44.1263
14	0.0717	0.0429	0.0909	0.0115	-0.056	0.055	0.0359	-0.2618	0.0202	0.1822	0.0281	-0.0838	-0.0003	0.0075	-0	0.1834	-0.0192	-0.006	0.2493	-0.0069	0.2219	67.451	44.4223	51.3457

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 48 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 49 through 70 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 71 through 96 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 97 through 122 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 123 through 144 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 145 through 183 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 20 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 21 through 48 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 49 through 70 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 71 through 96 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 97 through 106 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 107 through 157 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 158 through 172 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 173 through 183 )

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