PDB-5hyc: Structure based function annotation of a hypothetical protein MGG...

ID or keywords:

Entry

Database: PDB / ID: 5hyc

Title

Structure based function annotation of a hypothetical protein MGG_01005 related to the development of rice blast fungus

Components

Cytoplasmic dynein 1 intermediate chain 2
Uncharacterized protein

Keywords

UNKNOWN FUNCTION / dynein light chain Tctex-1 / Magnaporthe oryzae

Function / homology

Function and homology information

Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / : / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology

Biological species

Magnaporthe oryzae (rice blast fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Liu, J. / Li, G. / Huang, J. / Peng, Y.-l.

Citation

Journal: Sci Rep / Year: 2018
Title: Structure based function-annotation of hypothetical protein MGG_01005 from Magnaporthe oryzae reveals it is the dynein light chain orthologue of dynlt1/3.
Authors: Li, G. / Huang, J. / Yang, J. / He, D. / Wang, C. / Qi, X. / Taylor, I.A. / Liu, J. / Peng, Y.L.

History

Deposition	Feb 1, 2016	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 1, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 28, 2018	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5hyc.cif.gz	126.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5hyc.ent.gz	100.3 KB	Display	PDB format
PDBx/mmJSON format	5hyc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5hyc_validation.pdf.gz	447.2 KB	Display	wwPDB validaton report
Full document	5hyc_full_validation.pdf.gz	449 KB	Display
Data in XML	5hyc_validation.xml.gz	13 KB	Display
Data in CIF	5hyc_validation.cif.gz	17.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hy/5hyc ftp://data.pdbj.org/pub/pdb/validation_reports/hy/5hyc	HTTPS FTP

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Related structure data

Related structure data	5hxlSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3ogi-d 6gtm-3 5bw0-4 6gtm-1 6gtm-4 1u2l-2 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	#245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

C: Cytoplasmic dynein 1 intermediate chain 2

39 kDa, 3 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)	105.097, 105.097, 166.541
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-221- HOH
2	1	A-225- HOH
3	1	B-222- HOH
4	1	B-234- HOH
5	1	B-242- HOH

#1: Protein	Uncharacterized protein Mass: 17562.617 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) (fungus) Strain: 70-15 / ATCC MYA-4617 / FGSC 8958 / Gene: MGG_01005 / Production host: Escherichia coli (E. coli) / References: UniProt: G4NCW2
#2: Protein/peptide	Cytoplasmic dynein 1 intermediate chain 2 Mass: 3825.340 Da / Num. of mol.: 1 / Fragment: UNP residues 117-151 / Source method: obtained synthetically Source: (synth.) Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) (fungus) References: UniProt: G4MTS7
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.95 Å³/Da / Density % sol: 58.33 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: 2.0 M ammonium sulfate, 0.1M Bis-Tris(pH 5.2)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 2.4→29.63 Å / Num. obs: 18442 / % possible obs: 99 % / Redundancy: 25.1 % / Net I/σ(I): 28

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5hxl

5hxl

Resolution: 2.4→29.626 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.84

	R_factor	Num. reflection	% reflection
R_free	0.235	1844	10.01 %
R_work	0.2057	-	-
obs	0.2087	18421	98.93 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.4→29.626 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2147	0	0	76	2223

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2202
X-RAY DIFFRACTION	f_angle_d	1.194	2996
X-RAY DIFFRACTION	f_dihedral_angle_d	15.801	787
X-RAY DIFFRACTION	f_chiral_restr	0.052	334
X-RAY DIFFRACTION	f_plane_restr	0.008	383

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 (%)
2.4-2.4648	0.3378	138	0.2807	1243	X-RAY DIFFRACTION	99
2.4648-2.5373	0.3031	141	0.2585	1259	X-RAY DIFFRACTION	100
2.5373-2.6192	0.2644	140	0.2579	1260	X-RAY DIFFRACTION	99
2.6192-2.7127	0.2995	140	0.2581	1259	X-RAY DIFFRACTION	100
2.7127-2.8212	0.2872	138	0.2408	1244	X-RAY DIFFRACTION	98
2.8212-2.9495	0.2767	141	0.2334	1271	X-RAY DIFFRACTION	100
2.9495-3.1049	0.2488	141	0.2173	1273	X-RAY DIFFRACTION	100
3.1049-3.2992	0.2445	143	0.2112	1279	X-RAY DIFFRACTION	100
3.2992-3.5535	0.2011	141	0.1957	1276	X-RAY DIFFRACTION	100
3.5535-3.9104	0.2328	144	0.1804	1287	X-RAY DIFFRACTION	100
3.9104-4.4746	0.2093	143	0.1701	1290	X-RAY DIFFRACTION	98
4.4746-5.6312	0.2246	146	0.191	1307	X-RAY DIFFRACTION	100
5.6312-29.6287	0.2162	148	0.2102	1329	X-RAY DIFFRACTION	95

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	3.6307	-1.5453	0.9853	4.7051	-1.8473	4.0355	0.102	0.1078	-0.0594	-0.3499	-0.1463	0.3473	0.2591	-0.2086	0.0658	0.429	-0.1097	0.0044	0.4472	-0.0385	0.4245	-28.3588	-16.389	29.072
2	1.1497	-0.3913	-1.1027	3.7927	-2.5257	5.1288	-0.3946	-0.1873	-1.7289	0.5711	1.0686	1.2011	0.418	-0.4408	-0.5892	0.8831	-0.0039	-0.1404	1.3268	0.1807	1.0863	-42.334	-4.1367	13.1681
3	2.6559	-0.0744	0.7826	1.3616	0.5613	1.1128	-0.0999	-0.2187	-0.1013	0.1535	0.0172	0.0926	-0.1256	-0.0702	-0.0456	0.4178	-0.1043	0.0252	0.4747	0.0271	0.3917	-19.7556	-14.1701	41.038
4	2.5834	-1.4013	1.0052	2.3388	-0.3952	2.3548	-0.2519	-0.014	0.3011	0.1632	-0.1419	-0.1539	-0.3724	-0.3988	0.349	0.4398	-0.0188	-0.0395	0.4133	-0.0247	0.4929	-28.4898	-5.7612	33.1002
5	1.3143	-1.5083	-0.7824	5.0211	2.3458	1.144	-0.3266	0.6067	0.4156	0.8117	-0.2661	1.1432	-0.9831	0.9683	-0.3491	1.0503	-0.3209	-0.0837	0.727	0.2332	0.6077	-15.0614	3.5018	16.4884
6	0.7247	-0.2819	1.2705	0.7977	-1.1081	7.477	-0.3433	0.2277	0.1174	-0.0995	-0.2906	-0.4634	-1.2091	1.5038	0.2326	0.705	-0.266	-0.0492	0.6797	0.0834	0.5736	-7.4227	6.7307	30.9782
7	2.1955	2.7969	-1.7191	5.1465	-1.2695	2.5628	0.5787	-1.3438	0.2593	0.4866	-0.5111	0.2252	-0.4686	0.6421	0.0672	0.6264	-0.2055	0.1231	0.6411	-0.1226	0.438	-10.17	0.6233	48.7327
8	2.064	-1.2322	1.696	3.1724	-3.401	6.3254	-0.3269	-0.1627	0.7122	0.3211	0.3602	-0.0265	-1.9619	-0.4491	0.3316	0.7334	-0.1043	-0.0251	0.5109	-0.0867	0.6541	-16.833	8.4941	36.3282
9	5.9823	1.5743	5.1308	1.0514	1.4689	4.3223	1.3902	0.9415	0.4747	-0.145	-0.2323	0.3642	-0.2948	-1.5538	-0.2537	1.6776	-0.0772	-0.0398	1.1223	0.2118	0.8921	-20.3351	16.2566	18.5422
10	2.131	-1.0983	2.0401	1.3385	-1.149	3.847	0.1948	0.3773	0.5044	-0.4385	-0.5967	0.3486	-0.4733	0.8375	0.4187	0.6316	-0.0658	-0.131	0.403	0.0639	0.6196	-18.8528	1.6059	31.6763
11	3.4812	-4.0514	-2.4128	6.9864	2.1276	1.9549	-0.7256	-1.1026	-1.4042	1.0625	1.0378	-1.4284	1.9322	0.8212	0.5517	0.3017	-0.4517	-0.1951	0.4949	0.325	1.0572	-5.6113	-13.6551	43.7606
12	8.117	-6.6114	6.6074	7.4937	-5.9705	5.4547	-0.8093	1.2511	0.7604	-0.1897	-0.1389	-1.6138	-0.0648	-0.0388	0.359	0.4616	-0.1501	0.0744	0.6006	0.0557	0.5132	-15.4056	-12.5693	32.5699
13	5.6452	-3.3934	5.3773	2.2499	-3.8339	6.793	-0.5974	1.8575	1.3015	-0.4929	-0.217	-0.0726	0.2526	1.4366	0.5118	0.6169	-0.0874	-0.1492	0.4715	0.0933	0.5433	-24.8307	-5.5198	19.3112
14	8.8243	0.3743	-1.1591	6.9701	-0.5184	8.6467	0.3677	0.8765	-0.5247	-0.2939	-0.2797	-0.8605	-0.3106	-0.0054	-0.1873	1.0222	-0.2694	-0.2413	0.6803	0.1488	0.6265	-23.148	0.5925	12.5413
15	4.2893	-0.7507	4.8147	2.4	-1.7807	8.9998	0.3372	-0.0898	-0.0352	-0.6208	0.2238	0.0726	0.2664	0.2578	0.2415	0.64	-0.1334	0.1012	0.5925	0.0751	0.6373	-11.5884	-1.1608	27.7513
16	4.0336	-1.696	3.7755	0.8721	-0.789	6.1013	0.2992	0.2198	0.0769	-0.3481	-0.1211	0.0322	0.2136	0.3015	-0.0302	0.5196	-0.1913	-0.0437	0.46	0.0397	0.5374	-12.0556	-1.0492	32.693
17	0.2493	0.5032	0.2879	1.1021	0.6429	0.3799	-0.088	0.5222	0.6832	-0.1633	-0.1174	0.2528	-0.1313	-0.0616	-0.1144	1.0981	0.0312	-0.1067	0.6856	-0.0499	0.6329	-29.566	12.9913	27.7975
18	6.0486	-1.0402	1.6667	8.55	-4.5521	9.4981	-1.6273	1.141	-1.9034	-0.6656	0.3687	1.3233	-0.2799	-1.2682	0.8113	0.9391	-0.1523	0.1617	0.7596	-0.1876	0.7362	-26.0093	1.0755	39.0672
19	2.0014	-5.3969	6.334	4.642	-5.8552	7.4859	-0.5774	-0.587	-0.3482	0.4327	1.1085	1.4923	0.3829	-1.1734	-0.6049	0.4809	-0.0349	-0.0615	0.5395	-0.0135	0.5232	-19.8328	-8.2114	48.246
20	2.5697	-2.6144	-0.0501	2.6554	0.0894	0.5757	-0.9687	-0.3146	-0.4759	-0.2202	0.8352	0.3832	0.2671	-0.0111	-0.1103	0.6649	-0.0655	-0.0832	0.559	0.0822	0.5345	-13.8978	-21.6101	53.9332
21	1.6438	1.0417	-0.6972	7.447	-8.0087	9.8516	-0.6032	0.0184	-0.6934	0.5475	0.8033	0.3678	1.2028	-0.4802	-0.0814	0.9259	0.1915	0.1365	0.5885	0.0098	0.6316	-10.1813	-36.2559	66.3025

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 56 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 57 through 66 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 67 through 117 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 118 through 153 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 3 through 10 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 11 through 26 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 27 through 36 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 37 through 54 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 55 through 66 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 67 through 77 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 78 through 112 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 113 through 117 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 118 through 122 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 123 through 127 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 128 through 134 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 135 through 153 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 122 through 126 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 127 through 131 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 132 through 136 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 137 through 141 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 142 through 150 )

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