PDB-5v5f: Crystal structure of RICE1 (PNT2)

ID or keywords:

Entry

Database: PDB / ID: 5v5f

Title

Crystal structure of RICE1 (PNT2)

Components

At3g11770

Keywords

TRANSFERASE /

Nuclease / mi-RNA

Function / homology

Function and homology information

exoribonuclease II /

exoribonuclease II activity / RISC complex binding / single-stranded DNA 3'-5' DNA exonuclease activity / regulatory ncRNA-mediated gene silencing /

vacuole / vacuolar membrane / positive regulation of miRNA metabolic process / 3'-5' exonuclease activity / : ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.945 Å

Authors

Li, P.

Citation

Journal: Elife / Year: 2017
Title: RISC-interacting clearing 3'- 5' exoribonucleases (RICEs) degrade uridylated cleavage fragments to maintain functional RISC in Arabidopsis thaliana.
Authors: Zhang, Z. / Hu, F. / Sung, M.W. / Shu, C. / Castillo-Gonzalez, C. / Koiwa, H. / Tang, G. / Dickman, M. / Li, P. / Zhang, X.

History

Deposition	Mar 14, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 13, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5v5f.cif.gz	250.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5v5f.ent.gz	206.2 KB	Display	PDB format
PDBx/mmJSON format	5v5f.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v5/5v5f ftp://data.pdbj.org/pub/pdb/validation_reports/v5/5v5f	HTTPS FTP

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Related structure data

Similar structure data	2zts-1 2q3s-d 1vk0-d 6y8j-1 5vg3-d 5lkq-1 6y8s-1 4tl7-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: At3g11770

B: At3g11770

C: At3g11770

68.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: At3g11770

C: At3g11770

B: At3g11770

C: At3g11770

A: At3g11770

defined by author&software
Evidence: gel filtration
138 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	7_545	y+1/2,x-1/2,-z+1/2	1
crystal symmetry operation	10_655	-x+1,-y,z	1
crystal symmetry operation	16_555	-y+1/2,-x+1/2,-z+1/2	1

Unit cell

Length a, b, c (Å)	193.250, 193.250, 214.719
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4₁22

#1: Protein	At3g11770 / F26K24.6 protein / Polynucleotidyl transferase / ribonuclease H-like superfamily protein / Putative ...F26K24.6 protein / Polynucleotidyl transferase / ribonuclease H-like superfamily protein / Putative uncharacterized protein At3g11770 Mass: 22980.170 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: F26K24.6, At3g11770, AXX17_At3g11710 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SF21

#1: Protein

At3g11770 / F26K24.6 protein / Polynucleotidyl transferase / ribonuclease H-like superfamily protein / Putative ...

Mass: 22980.170 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Arabidopsis thaliana (thale cress) / Gene: F26K24.6, At3g11770, AXX17_At3g11710 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q9SF21

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 7.4 Å³/Da / Density % sol: 83.08 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion / pH: 7.5 Details: 30% pentaerylthritol proxylate (5/4 PO/OH), 0.2 M KCl, 50 mM HEPES.

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Data collection

Diffraction	Mean temperature: 120 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.945→50 Å / Num. obs: 42979 / % possible obs: 0.998 % / Redundancy: 8.2 % / Net I/σ(I): 20.9

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Processing

Software

Name	Version	Classification
PHENIX	1.8.1_1168	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHENIX		phasing

Refinement

Resolution: 2.945→49.963 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1

	R_factor	Num. reflection	% reflection
R_free	0.1946	1999	4.65 %
R_work	0.1685	-	-
obs	0.1697	42953	99.69 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.945→49.963 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4857	0	0	0	4857

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4968
X-RAY DIFFRACTION	f_angle_d	1.139	6723
X-RAY DIFFRACTION	f_dihedral_angle_d	16.215	1788
X-RAY DIFFRACTION	f_chiral_restr	0.082	741
X-RAY DIFFRACTION	f_plane_restr	0.004	846

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 (%)
2.9453-3.019	0.3242	138	0.2645	2828	X-RAY DIFFRACTION	98
3.019-3.1006	0.2757	141	0.2432	2891	X-RAY DIFFRACTION	100
3.1006-3.1918	0.2414	140	0.2317	2867	X-RAY DIFFRACTION	100
3.1918-3.2948	0.2367	142	0.2071	2909	X-RAY DIFFRACTION	100
3.2948-3.4126	0.2004	143	0.1825	2911	X-RAY DIFFRACTION	100
3.4126-3.5492	0.1741	141	0.1651	2901	X-RAY DIFFRACTION	100
3.5492-3.7106	0.2044	142	0.1623	2908	X-RAY DIFFRACTION	100
3.7106-3.9062	0.22	141	0.1674	2905	X-RAY DIFFRACTION	100
3.9062-4.1508	0.1639	143	0.1506	2932	X-RAY DIFFRACTION	100
4.1508-4.4711	0.1446	143	0.1308	2929	X-RAY DIFFRACTION	100
4.4711-4.9207	0.1533	144	0.1294	2939	X-RAY DIFFRACTION	100
4.9207-5.6319	0.1873	143	0.153	2948	X-RAY DIFFRACTION	100
5.6319-7.0924	0.2263	146	0.183	2988	X-RAY DIFFRACTION	100
7.0924-49.9701	0.1811	152	0.1649	3098	X-RAY DIFFRACTION	99

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	0.6988	-0.5086	0.3187	0.3714	-0.236	0.1493	-0.2962	-0.2235	0.2663	0.1721	0.2725	0.1648	-0.2946	-0.452	-0.0457	0.2878	0.0183	0.124	0.7672	-0.035	0.4273	57.6791	7.8949	78.0275
2	0.1798	0.0457	-0.0423	0.2036	0.009	0.4102	-0.0449	-0.0774	-0.0127	0.0382	-0.1322	0.0397	-0.2839	-0.2071	-0.0258	0.2577	-0.0297	0.1044	0.5462	0.0548	0.3711	67.5608	2.6116	70.4916
3	0.0368	-0.016	0.0488	0.3128	0.051	0.1136	0.266	0.1272	0.2654	0.3238	-0.2486	-0.0278	-0.1051	-0.0245	0.0241	0.2571	0.0359	0.1168	0.5619	0.0356	0.3958	70.3854	5.2744	75.1658
4	0.1168	-0.0031	0.0096	0.0098	0.0424	0.3085	-0.1697	-0.1036	-0.2425	-0.0432	0.0364	-0.0611	0.0569	-0.2443	-0.0059	0.2474	-0.0413	0.0963	0.4958	0.0292	0.3659	64.9736	-8.3231	63.5818
5	0.113	-0.0643	0.2642	0.1977	0.1004	1.0806	0.0002	-0.0497	-0.1646	0.0307	-0.1411	0.1593	-0.2929	-0.2841	-0.1243	0.0908	-0.0264	0.1417	0.7048	0.0408	0.4325	52.0577	0.8519	65.3468
6	0.652	-0.2135	0.1462	0.2215	-0.1601	0.1213	-0.2188	-0.5013	-0.2324	0.3089	0.2046	-0.1512	-0.0987	-0.0601	0.0418	0.5294	-0.028	-0.0657	0.6593	-0.1699	0.3274	108.9002	19.1442	94.8475
7	0.226	0.0833	0.0343	0.1239	0.0503	0.0215	-0.1294	-0.2777	0.1731	0.1277	0.0668	-0.1288	-0.47	-0.0861	-0.0188	0.6175	0.0103	-0.108	0.4574	-0.1684	0.2955	104.3114	28.2753	88.5943
8	0.1874	-0.0195	-0.0238	0.039	-0.0115	0.0867	-0.0902	-0.0768	-0.0487	0.0873	-0.0329	0.2857	-0.0721	0.1271	-0	0.3152	-0.0155	-0.0148	0.3485	-0.0848	0.3353	109.1118	9.9311	78.5264
9	0.2041	-0.1994	0.0859	0.2806	-0.1183	0.052	0.2171	-0.1275	-0.0581	0.5214	0.0305	0.3155	-0.0318	0.074	0.0173	0.4199	0.0244	-0.0252	0.4209	-0.1	0.3447	101.9339	15.8288	83.9808
10	0.0565	0.0216	-0.0704	0.1938	-0.0258	0.1984	-0.1462	-0.1598	0.069	-0.1141	0.0887	-0.029	-0.2045	0.167	0	0.3652	-0.0801	-0.0372	0.3783	-0.0605	0.3667	116.4603	20.1991	73.1652
11	0.631	-0.1999	-0.5844	0.4008	0.1959	0.5433	-0.1849	-0.0723	-0.053	0.2272	-0.0571	-0.1601	0.061	0.2678	-0.0493	0.3828	-0.0949	-0.1514	0.6046	-0.0259	0.445	126.7002	12.2079	89.7554
12	0.1766	-0.1008	-0.1054	0.0867	0.0291	0.0946	-0.3026	-0.0544	0.3516	0.0237	0.2563	0.0527	-0.0977	0.1734	-0.0181	0.4676	-0.1434	-0.1161	0.523	-0.0537	0.4451	119.5535	22.157	86.1129
13	0.0439	-0.0121	0.1062	0.4956	0.6412	1.1752	0.0909	-0.2275	0.0061	0.371	-0.0574	0.1521	-0.5596	-0.5483	0.175	0.7459	0.1713	0.0103	0.3646	-0.1362	0.6493	85.6131	42.5304	70.1078
14	0.2387	0.0466	0.3262	0.0238	0.1204	0.569	-0.0398	-0.2951	-0.0439	-0.0676	0.1139	-0.143	-0.2905	-0.2433	0.0257	0.4947	0.0687	0.0411	0.2412	0.029	0.4012	91.771	31.5898	64.8252
15	0.1141	-0.1471	-0.1149	0.5126	-0.1176	0.311	-0.0218	-0.1023	0.4197	0.097	0.226	0.4938	-0.1259	-0.3024	0.2061	0.5921	0.1435	0.0509	0.2549	-0.0378	0.4108	86.2218	31.6471	62.4092
16	0.1065	-0.1018	-0.0438	0.105	0.0662	0.1315	-0.0214	-0.1605	0.0329	-0.3123	0.0285	-0.2819	-0.1543	0.1126	0.0001	0.4467	-0.0622	0.0247	0.2763	0.0095	0.3923	101.5473	29.8488	59.605
17	0.317	0.0217	0.0915	0.1071	-0.1711	0.3419	-0.0718	-0.3265	0.2319	0.0983	0.1334	0.0252	-0.4505	0.1837	0.0039	0.6418	-0.0442	0.0561	0.3152	-0.1028	0.5016	103.4482	39.4759	74.5788

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 30 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 31 through 74 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 75 through 99 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 100 through 158 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 159 through 200 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 30 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 31 through 44 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 45 through 74 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 75 through 99 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 100 through 158 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 159 through 176 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 177 through 200 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 1 through 30 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 31 through 74 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 75 through 99 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 100 through 140 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 141 through 200 )

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