PDB-5ee0: Crystal structure of OsYchF1 at pH 6.5

ID or keywords:

Entry

Database: PDB / ID: 5ee0

Title

Crystal structure of OsYchF1 at pH 6.5

Components

Obg-like ATPase 1

Keywords

HYDROLASE / OSYCHF1 /

GTP-BINDING PROTEIN / AMP-PNP / YCHF-TYPE / P-LOOP NTPASE / ATP-BINDING PROTEIN

Function / homology

Function and homology information

negative regulation of response to salt stress / negative regulation of defense response to bacterium /

ribosomal large subunit binding / response to salt stress /

Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement /

GTPase activity / GTP binding /

ATP hydrolysis activity /

ATP binding /

metal ion binding ...
Similarity search - Function

Biological species

Oryza sativa subsp. japonica (Japanese rice)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Li, X. / Chen, Z.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: ATP binding by the P-loop NTPase OsYchF1 (an unconventional G protein) contributes to biotic but not abiotic stress responses
Authors: Cheung, M.-Y. / Li, X. / Miao, R. / Fong, Y.-H. / Li, K.-P. / Yung, Y.-L. / Yu, M.-H. / Wong, K.-B. / Chen, Z. / Lam, H.-M.

History

Deposition	Oct 22, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 24, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 23, 2016	Group: Database references
Revision 1.2	Feb 19, 2020	Group: Data collection / Database references / Derived calculations Category: citation / diffrn_source / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	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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PDBx/mmCIF format	5ee0.cif.gz	159.4 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ee/5ee0 ftp://data.pdbj.org/pub/pdb/validation_reports/ee/5ee0	HTTPS FTP

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Related structure data

Related structure data	5ee1C 5ee3C 5ee9C 2ohfS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5ee9-2 5ee3-2 5ee1-d 2dby-d 3dpn-1 4i76-1 1ni3-d 5yev-3 4r0y-1 5ee9-1 Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (4) #117 - Sep 2009 Xanthine Oxidoreductase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #82 - Oct 2006 Cytochrome p450 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Obg-like ATPase 1

44.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	58.618, 66.930, 66.945
Angle α, β, γ (deg.)	90.00, 112.67, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Obg-like ATPase 1 / Ribosome-binding ATPase YchF / OsYchF1 Mass: 44485.887 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: OS08G0199300, OSYCHF1 / Plasmid: PRSETA-HISSUMO / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q6Z1J6, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Obg-like ATPase 1 / Ribosome-binding ATPase YchF / OsYchF1

Mass: 44485.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Oryza sativa subsp. japonica (Japanese rice)
Gene: OS08G0199300, OSYCHF1 / Plasmid: PRSETA-HISSUMO / Production host:

ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q6Z1J6,

Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.72 Å³/Da / Density % sol: 54.84 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG, 0.2M MGCL2, PH 6.5

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Data collection

Diffraction	Mean temperature: 130 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 11, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. obs: 23625 / % possible obs: 97.3 % / Observed criterion σ(I): 3 / Redundancy: 4.8 % / R_merge(I) obs: 0.077 / R_sym value: 0.052 / Net I/σ(I): 19
Reflection shell	Resolution: 2.21→2.25 Å / R_merge(I) obs: 0.59 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing
REFMAC	5.7.0029	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2OHF

2ohf

Resolution: 2.2→32.84 Å / Cor.coef. F_o:F_c: 0.907 / Cor.coef. F_o:F_c free: 0.9 / SU B: 11.723 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.415 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.259	939	5.1 %	RANDOM
R_work	0.235	-	-	-
obs	0.236	17505	75.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 38.21 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.73 Å²	0 Å²	-1.82 Å²
2-	-	-1.29 Å²	-0 Å²
3-	-	-	2.8 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→32.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2832	0	0	112	2944

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	2896
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2718
X-RAY DIFFRACTION	r_angle_refined_deg	1.127	1.95	3920
X-RAY DIFFRACTION	r_angle_other_deg	0.737	3	6254
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.19	5	362
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.343	24.511	133
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.142	15	482
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.649	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	437
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	3282
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	659
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.2→2.26 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.41	21	-
R_work	0.32	569	-
obs	-	-	32.65 %

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	4.7843	1.1257	-1.8338	0.5748	-0.2257	2.1276	-0.1014	-0.2553	0.1646	0.1968	0.1366	0.0436	0.1908	0.2797	-0.0352	0.2432	0.0523	0.0235	0.2398	-0.0218	0.0679	2.6718	4.165	29.7852
2	2.9531	-0.9977	-0.0636	2.434	-0.7055	1.7813	0.0354	-0.005	0.8751	-0.0903	0.0135	-0.049	0.3159	-0.2604	-0.0489	0.1103	-0.0473	0.0107	0.0939	-0.0042	0.2909	-18.4618	5.7655	21.5398
3	2.0661	2.7609	0.6597	7.4904	4.8818	4.6912	-0.1947	-0.2129	-0.0165	0.182	-0.2644	0.1286	0.3619	-0.0514	0.4591	0.1652	-0.0041	-0.0091	0.0303	-0.0059	0.3504	-13.4238	15.557	36.6139
4	0.445	-0.6337	0.0416	1.4059	-0.9077	4.2797	-0.1834	-0.0214	-0.056	0.2036	0.1017	-0.1566	-0.1149	-0.2388	0.0818	0.0987	-0.0117	0.0701	0.1596	-0.0069	0.1528	-13.8379	-0.786	39.8348
5	0.5978	-0.6084	0.0147	1.8038	-2.9133	10.3326	-0.1936	-0.0857	0.109	0.2229	0.0705	0.0152	-0.2715	-0.2453	0.1231	0.1318	0.0369	-0.0173	0.1193	-0.0223	0.1394	-12.9497	2.6539	40.8287
6	5.9961	5.9388	-8.1282	24.2198	6.9162	23.6309	-0.2554	0.2479	-0.1623	-0.4738	0.1743	-0.2253	0.4507	-0.2205	0.0811	0.2171	0.1179	-0.0492	0.1361	0.0336	0.1467	-7.9152	12.8883	10.8536
7	3.0474	1.392	-0.0455	3.1646	0.2954	0.0412	-0.1734	0.4195	0.2538	-0.5869	0.1942	-0.0521	-0.0629	0.0068	-0.0208	0.1787	-0.0565	0.0596	0.2288	0.0756	0.0799	-9.6317	5.7617	17.2363
8	4.0225	-5.0874	6.7586	6.9869	-9.2638	12.3039	-0.1154	-0.2333	-0.4272	-0.0916	0.2506	0.0994	0.0897	-0.4256	-0.1351	0.2104	0.0922	0.0697	0.2741	-0.0304	0.5092	-28.9477	0.557	2.535
9	23.2104	4.8396	-1.1762	1.0702	0.1692	5.2443	0.2123	0.1599	-0.4545	0.0098	-0.0265	-0.156	-0.0512	-0.0264	-0.1858	0.1176	0.0581	0.051	0.1611	0.066	0.1002	-13.4294	-3.0657	6.4532
10	9.5029	6.678	-2.2231	4.9629	-1.1023	1.3542	-0.0028	0.5664	0.3822	-0.0695	0.1979	0.1748	-0.1	-0.3565	-0.1951	0.0985	0.0797	0.0783	0.3907	0.2073	0.1302	4.3615	7.2616	9.2352
11	8.9677	4.3804	4.0366	2.4094	1.0001	5.8387	0.0615	0.2728	-0.5694	0.159	0.275	-0.3175	-0.4525	-0.1956	-0.3365	0.127	0.0804	0.0555	0.2105	-0.0141	0.3292	23.5541	11.25	14.7435
12	2.9523	0.2475	-0.3376	0.0461	-0.269	3.0131	0.0179	0.3201	-0.1878	-0.0218	-0.0255	-0.0308	0.2241	0.1133	0.0075	0.0637	0.0307	0.0772	0.2234	0.0415	0.1551	10.1541	-1.5686	13.7188
13	2.965	0.7157	0.5244	0.5792	0.0864	0.5372	0.1549	0.2067	-0.0567	-0.0186	-0.0807	0.0081	0.1517	0.1025	-0.0742	0.1181	0.0283	0.031	0.1518	0.012	0.0719	-10.2972	-5.7678	16.5381
14	6.4413	-0.6328	-0.9314	0.5338	0.0856	1.1455	0.0499	-0.1913	0.1037	-0.0899	0.0421	0.046	0.0322	-0.1224	-0.092	0.0845	-0.0313	0.0568	0.1121	0.015	0.0924	-26.2489	-3.9434	26.8205
15	1.2684	-0.7343	0.6542	0.515	-0.3187	0.4709	0.0133	0.0081	-0.0726	0.0453	0.0696	0.0052	0.1003	-0.0557	-0.0829	0.1543	-0.0129	0.0531	0.1892	0.0077	0.1156	-13.6734	-4.2501	35.0369
16	2.0341	-0.3035	-0.1064	2.2831	-0.4226	1.6524	-0.2071	-0.0387	0.1605	0.1346	0.0382	-0.1612	-0.1361	0.1206	0.1689	0.1083	0.0356	0.0004	0.1103	0.0039	0.0596	1.7775	0.274	46.4366
17	9.6137	-2.1545	4.1251	6.0437	2.3302	8.9735	-0.3055	-0.6232	-0.7316	0.4074	0.1337	-0.0032	0.5961	0.0542	0.1719	0.2259	0.1015	0.1012	0.1367	0.1231	0.1457	-4.7365	-15.4936	54.8296
18	3.6654	1.9743	1.1499	4.5026	-0.8192	1.0478	-0.2115	-0.0067	-0.0196	0.2406	-0.0126	-0.3061	-0.1305	0.0896	0.2241	0.1412	0.1013	0.0693	0.2258	0.0628	0.1554	3.9673	-4.2529	50.0015

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	16 - 26
2	X-RAY DIFFRACTION	2	A	27 - 47
3	X-RAY DIFFRACTION	3	A	48 - 61
4	X-RAY DIFFRACTION	4	A	62 - 78
5	X-RAY DIFFRACTION	5	A	79 - 95
6	X-RAY DIFFRACTION	6	A	96 - 110
7	X-RAY DIFFRACTION	7	A	111 - 129
8	X-RAY DIFFRACTION	8	A	130 - 140
9	X-RAY DIFFRACTION	9	A	141 - 148
10	X-RAY DIFFRACTION	10	A	149 - 167
11	X-RAY DIFFRACTION	11	A	168 - 185
12	X-RAY DIFFRACTION	12	A	186 - 211
13	X-RAY DIFFRACTION	13	A	212 - 255
14	X-RAY DIFFRACTION	14	A	256 - 282
15	X-RAY DIFFRACTION	15	A	283 - 314
16	X-RAY DIFFRACTION	16	A	315 - 351
17	X-RAY DIFFRACTION	17	A	352 - 366
18	X-RAY DIFFRACTION	18	A	367 - 387

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