PDB-5aon: Crystal structure of the conserved N-terminal domain of Pex14 fro...

ID or keywords:

Entry

Database: PDB / ID: 5aon

Title

Crystal structure of the conserved N-terminal domain of Pex14 from Trypanosoma brucei

Components

PEROXIN 14

Keywords

SIGNALING PROTEIN / PEROXISOMAL MATRIX PROTEIN IMPORT RECEPTOR

Function / homology

Function and homology information

glycosome membrane / protein import into peroxisome matrix, docking / protein targeting to vacuole / glycosome / post-transcriptional regulation of gene expression
Similarity search - Function

Biological species

TRYPANOSOMA BRUCEI (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.646 Å

Authors

Obita, T. / Sugawara, Y. / Mizuguchi, M. / Watanabe, Y. / Kawaguchi, K. / Imanaka, T.

Citation

Journal: FEBS Lett. / Year: 2016
Title: Characterization of the Interaction between Trypanosoma Brucei Pex5P and its Receptor Pex14P.
Authors: Watanabe, Y. / Kawaguchi, K. / Okuyama, N. / Sugawara, Y. / Obita, T. / Mizuguchi, M. / Morita, M. / Imanaka, T.

History

Deposition	Sep 11, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 23, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jan 27, 2016	Group: Database references
Revision 1.2	Feb 10, 2016	Group: Database references
Revision 1.3	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5aon.cif.gz	112.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5aon.ent.gz	91.2 KB	Display	PDB format
PDBx/mmJSON format	5aon.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5aon_validation.pdf.gz	459.8 KB	Display	wwPDB validaton report
Full document	5aon_full_validation.pdf.gz	460.4 KB	Display
Data in XML	5aon_validation.xml.gz	12.7 KB	Display
Data in CIF	5aon_validation.cif.gz	18.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ao/5aon ftp://data.pdbj.org/pub/pdb/validation_reports/ao/5aon	HTTPS FTP

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Related structure data

Related structure data	3ff5S S: Starting model for refinement
Similar structure data	6kmc-2 6lji-1 5bmg-2 1fd6-d 2zw1-d 2kdm-d 6nl9-2 6l9b-d 4e7v-12 6nl6-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

3ff5S

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: PEROXIN 14

B: PEROXIN 14

C: PEROXIN 14

D: PEROXIN 14

E: PEROXIN 14

hetero molecules

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

1

A: PEROXIN 14

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

2

B: PEROXIN 14

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

3

C: PEROXIN 14

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

4

D: PEROXIN 14

hetero molecules

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

5

E: PEROXIN 14

hetero molecules

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

Unit cell

Length a, b, c (Å)	53.569, 53.569, 342.827
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

#1: Protein	PEROXIN 14 / PEX14 Mass: 5948.788 Da / Num. of mol.: 5 / Fragment: CONSERVED N-TERMINAL DOMAIN, UNP RESIDUES 23-71 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: Q8IEW2
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49 % / Description: NONE
Crystal grow	pH: 8.5 Details: 21% PEG3350, 0.5M AMMONIUM SULFATE, 0.1M TRIS-HCL PH8.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1
Detector	Type: DECTRIS / Date: Jun 14, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.65→27.57 Å / Num. obs: 37178 / % possible obs: 100 % / Observed criterion σ(I): 1.6 / Redundancy: 17.4 % / B_iso Wilson estimate: 24.64 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 24.3
Reflection shell	Resolution: 1.65→1.74 Å / Redundancy: 18.3 % / R_merge(I) obs: 0.48 / Mean I/σ(I) obs: 6.2 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FF5

3ff5

Resolution: 1.646→27.571 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 21.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2316	1848	5 %
R_work	0.1953	-	-
obs	0.1971	37018	99.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.646→27.571 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1934	0	15	196	2145

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	1988
X-RAY DIFFRACTION	f_angle_d	0.899	2661
X-RAY DIFFRACTION	f_dihedral_angle_d	12.762	776
X-RAY DIFFRACTION	f_chiral_restr	0.035	303
X-RAY DIFFRACTION	f_plane_restr	0.004	339

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 (%)
1.646-1.6905	0.3274	135	0.2316	2646	X-RAY DIFFRACTION	100
1.6905-1.7402	0.2768	159	0.2225	2597	X-RAY DIFFRACTION	100
1.7402-1.7964	0.226	131	0.215	2652	X-RAY DIFFRACTION	100
1.7964-1.8606	0.2306	150	0.2027	2616	X-RAY DIFFRACTION	100
1.8606-1.935	0.2512	120	0.1926	2662	X-RAY DIFFRACTION	100
1.935-2.0231	0.2333	159	0.2078	2618	X-RAY DIFFRACTION	100
2.0231-2.1297	0.2098	119	0.1957	2704	X-RAY DIFFRACTION	100
2.1297-2.2631	0.2501	130	0.1857	2679	X-RAY DIFFRACTION	100
2.2631-2.4377	0.2007	147	0.1909	2708	X-RAY DIFFRACTION	100
2.4377-2.6829	0.2468	133	0.1968	2712	X-RAY DIFFRACTION	100
2.6829-3.0706	0.2625	146	0.208	2742	X-RAY DIFFRACTION	100
3.0706-3.867	0.2144	140	0.1888	2825	X-RAY DIFFRACTION	100
3.867-27.5752	0.2221	179	0.1888	3009	X-RAY DIFFRACTION	100

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	3.4183	-1.9776	0.7462	6.5646	-0.0006	4.5162	0.0104	-0.0333	-0.1724	-0.0794	-0.1024	0.4315	0.0371	-0.572	0.0775	0.2886	-0.0052	0.0115	0.1926	0.0209	0.1566	28.4001	35.4385	10.8108
2	5.1944	3.3475	-0.7661	6.9108	4.1328	4.8401	-0.1588	-0.2957	0.0789	0.2892	0.1222	0.0145	0.2217	0.1998	0.0053	0.3286	0.0869	-0.0115	0.1432	0.0142	0.1746	35.7256	34.8141	16.7927
3	7.065	-2.8505	3.8967	3.1136	-3.1626	3.5116	-0.0551	0.3993	0.2382	-0.1083	-0.02	-0.1311	0.5575	0.0618	0.034	0.3024	0.0151	0.0089	0.154	0.0235	0.189	36.2511	33.6561	6.1004
4	4.7443	4.6761	-4.6134	4.6859	-4.609	6.536	-0.2325	0.1028	-0.7438	-0.3401	0.1753	-0.0563	0.8906	-0.3491	-0.0213	0.4022	0.0244	0.0179	0.2577	0.0607	0.3528	27.8027	31.21	31.1788
5	4.1916	-2.2621	4.2566	4.0624	-4.3041	5.7397	-0.1355	-0.0721	0.4324	-0.1995	0.0773	0.2786	-0.2884	0.2395	-0.0094	0.2497	0.0461	0.0185	0.2145	0.0141	0.2215	37.5867	42.8334	25.6009
6	5.8552	3.4006	-3.9663	3.241	-3.7155	7.0673	0.0926	0.1232	-0.0513	-0.6148	-0.1127	-0.0819	0.2614	-0.2808	0.0024	0.2308	0.0461	-0.0197	0.1667	-0.014	0.1715	25.4675	38.8696	22.5687
7	9.2385	5.9699	2.6797	9.4187	6.0476	4.2712	0.0165	-0.0569	-0.0488	0.4693	0.0588	0.1128	0.1517	-0.1325	-0.1411	0.2981	0.0693	0.0201	0.2449	0.0537	0.1986	23.7577	39.3127	32.723
8	6.8613	-5.5914	0.2342	5.9745	1.4463	2.0339	0.4291	1.1288	0.7673	-1.1728	-1.0837	-1.257	0.107	1.0238	0.3125	0.3943	0.1927	0.1418	0.4541	0.2183	0.4627	49.9027	37.1941	36.1787
9	7.1144	0.6554	-4.8458	9.26	-1.9339	6.8042	0.0518	-0.0118	0.9146	-0.4687	-0.1728	-0.4655	-0.4341	-0.3087	0.0812	0.3315	0.1094	-0.0332	0.2162	0.006	0.3287	36.6407	46.7764	36.6143
10	3.4845	-3.8147	-1.003	4.2621	1.3295	1.4227	-0.0408	0.1247	-0.3485	-0.1545	-0.1641	0.0416	0.6991	0.0307	0.0823	0.3423	0.1175	-0.0001	0.204	0.02	0.1978	38.9837	33.4202	38.0478
11	7.7558	2.7341	1.2923	2.0646	-0.7982	7.6279	0.0168	0.118	0.2876	0.2529	-0.4855	-0.2546	-0.2297	0.3204	0.3609	0.2832	0.1294	-0.0138	0.2582	0.0619	0.2938	47.0182	37.0387	44.7123
12	1.6452	-2.0042	0.2935	8.0005	-0.2948	7.8422	0.0896	0.1279	1.0437	0.0953	-0.4295	-1.8845	-0.5249	1.0692	0.168	0.2529	-0.0456	-0.0377	0.2627	0.0969	0.5488	53.7026	42.1713	10.3099
13	7.4336	1.1933	0.3437	2.5992	-2.0964	1.9458	-0.2792	0.2309	1.0416	-0.3391	0.2732	0.516	-1.4522	-0.0726	-0.0799	0.5532	0.0388	0.0284	0.2127	0.069	0.4808	41.5632	52.2798	6.2209
14	3.8042	-4.8699	1.7222	7.4322	-0.505	3.1289	-0.1824	0.3231	0.3798	-0.0772	-0.115	-0.4399	-0.0014	0.3563	0.2164	0.2859	0.0087	0.0005	0.18	0.1118	0.3006	44.5695	40.1464	2.5987
15	8.8622	2.114	-1.1514	8.5357	4.6677	5.8078	0.0876	-0.1561	0.2684	0.4103	-0.2001	-0.1187	0.0347	0.2152	0.115	0.302	0.0439	-0.0481	0.1295	0.0527	0.2339	45.9234	38.5965	13.4359
16	8.9412	4.9904	-0.989	4.7922	-3.3009	4.1496	0.1002	-0.4889	0.4887	1.5202	-0.419	0.8744	0.406	-0.9102	0.0539	0.6675	-0.1654	0.1566	0.2918	-0.0614	0.282	15.5385	32.1907	-0.6587
17	4.5377	-3.9376	0.4737	7.519	1.3925	6.5948	-0.3015	-0.134	0.0225	-0.0848	0.3994	-0.0994	-0.3159	0.2121	-0.1044	0.356	-0.0584	0.03	0.1777	-0.0244	0.2245	27.8711	41.4723	-2.929
18	2.4021	2.5802	-1.8719	3.6839	-2.8719	2.286	0.7624	-0.8808	-0.5394	0.906	-0.7886	-0.5571	0.9905	0.0997	0.3464	0.5869	-0.2228	-0.0966	0.2416	0.129	0.2816	26.0459	28.0829	-2.026
19	5.3914	-2.3248	3.0317	8.573	-0.8243	8.6078	-0.0563	-0.0809	0.1274	0.1828	-0.1251	0.0971	-0.5179	-0.5187	0.2008	0.363	-0.0571	0.0597	0.1661	-0.0269	0.1962	17.8957	30.4055	-8.8296

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 23 THROUGH 45 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 46 THROUGH 59 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 60 THROUGH 71 )
4	X-RAY DIFFRACTION	4	CHAIN 'B' AND (RESID 23 THROUGH 37 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 38 THROUGH 45 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 46 THROUGH 59 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 60 THROUGH 71 )
8	X-RAY DIFFRACTION	8	CHAIN 'C' AND (RESID 23 THROUGH 37 )
9	X-RAY DIFFRACTION	9	CHAIN 'C' AND (RESID 38 THROUGH 45 )
10	X-RAY DIFFRACTION	10	CHAIN 'C' AND (RESID 46 THROUGH 59 )
11	X-RAY DIFFRACTION	11	CHAIN 'C' AND (RESID 60 THROUGH 71 )
12	X-RAY DIFFRACTION	12	CHAIN 'D' AND (RESID 23 THROUGH 37 )
13	X-RAY DIFFRACTION	13	CHAIN 'D' AND (RESID 38 THROUGH 45 )
14	X-RAY DIFFRACTION	14	CHAIN 'D' AND (RESID 46 THROUGH 59 )
15	X-RAY DIFFRACTION	15	CHAIN 'D' AND (RESID 60 THROUGH 71 )
16	X-RAY DIFFRACTION	16	CHAIN 'E' AND (RESID 24 THROUGH 37 )
17	X-RAY DIFFRACTION	17	CHAIN 'E' AND (RESID 38 THROUGH 45 )
18	X-RAY DIFFRACTION	18	CHAIN 'E' AND (RESID 46 THROUGH 59 )
19	X-RAY DIFFRACTION	19	CHAIN 'E' AND (RESID 60 THROUGH 71 )

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