PDB-8z7a: Open Barrel Structure of Translin from Trichoderma virens

ID or keywords:

Entry

Database: PDB / ID: 8z7a

Title

Open Barrel Structure of Translin from Trichoderma virens

Components

Translin

Keywords

DNA BINDING PROTEIN / Translin / C3PO / Trichoderma virens

Function / homology

Function and homology information

RNA metabolic process / single-stranded DNA binding / sequence-specific DNA binding / RNA binding / nucleus
Similarity search - Function

Biological species

Hypocrea virens (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 Å

Authors

Kumari, S. / Gupta, G.D.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: Open Barrel Structure of Translin from Trichoderma virens
Authors: Kumari, S. / Gupta, G.D.

History

Deposition	Apr 19, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 23, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8z7a.cif.gz	718.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8z7a.ent.gz	602.8 KB	Display	PDB format
PDBx/mmJSON format	8z7a.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/z7/8z7a ftp://data.pdbj.org/pub/pdb/validation_reports/z7/8z7a	HTTPS FTP

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Related structure data

Similar structure data	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: Translin

B: Translin

C: Translin

D: Translin

E: Translin

F: Translin

G: Translin

H: Translin

245 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	76.552, 153.223, 103.949
Angle α, β, γ (deg.)	90.00, 111.47, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Translin Mass: 30625.578 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hypocrea virens (strain Gv29-8 / FGSC 10586) (fungus) Gene: TRIVIDRAFT_72774 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: G9MJL3
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.65 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 18% PEG 1450, 0.18M Magnesium Chloride, 0.1M sodium cacodylate pH 6.8

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9795 Å
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 6, 2018
Radiation	Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 3.2→41.51 Å / Num. obs: 36769 / % possible obs: 99.9 % / Redundancy: 3.8 % / CC_1/2: 0.999 / R_merge(I) obs: 0.072 / R_pim(I) all: 0.043 / R_rim(I) all: 0.084 / Χ²: 0.5 / Net I/σ(I): 10.9 / Num. measured all: 141391
Reflection shell	Resolution: 3.2→3.34 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.496 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4492 / CC_1/2: 0.841 / R_pim(I) all: 0.293 / R_rim(I) all: 0.576 / Χ²: 0.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.19.1_4122: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.2→38.28 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.43 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2369	1779	4.85 %
R_work	0.2129	-	-
obs	0.2141	36687	99.71 %

Solvent computation

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

Displacement parameters

B_iso mean: 75 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→38.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14305	0	0	7	14312

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	14539
X-RAY DIFFRACTION	f_angle_d	0.512	19720
X-RAY DIFFRACTION	f_dihedral_angle_d	3.634	1967
X-RAY DIFFRACTION	f_chiral_restr	0.036	2353
X-RAY DIFFRACTION	f_plane_restr	0.004	2498

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 (%)
3.2-3.29	0.3907	138	0.3459	2648	X-RAY DIFFRACTION	100
3.29-3.38	0.3142	139	0.3029	2667	X-RAY DIFFRACTION	100
3.38-3.49	0.2983	143	0.2641	2721	X-RAY DIFFRACTION	100
3.49-3.62	0.287	139	0.2387	2639	X-RAY DIFFRACTION	100
3.62-3.76	0.243	146	0.241	2685	X-RAY DIFFRACTION	100
3.76-3.93	0.2796	107	0.2626	2702	X-RAY DIFFRACTION	100
3.93-4.14	0.2542	150	0.2005	2675	X-RAY DIFFRACTION	100
4.14-4.4	0.2138	145	0.1921	2677	X-RAY DIFFRACTION	100
4.4-4.74	0.2371	124	0.1836	2719	X-RAY DIFFRACTION	100
4.74-5.21	0.205	145	0.2005	2665	X-RAY DIFFRACTION	100
5.21-5.97	0.2416	140	0.2278	2702	X-RAY DIFFRACTION	100
5.97-7.51	0.1928	135	0.2161	2707	X-RAY DIFFRACTION	100
7.51-38.28	0.1818	128	0.1515	2701	X-RAY DIFFRACTION	98

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	1.3792	0.9703	-0.2965	1.2976	-0.3394	2.9625	0.0767	-0.2585	0.2339	0.5451	-0.0552	-0.0228	-0.2668	-0.0885	0.0871	0.5515	-0.0617	-0.0814	0.5651	0.0539	0.7644	64.2229	29.6259	39.4399
2	1.7306	-0.2692	-0.2071	2.3871	-1.1882	3.1421	-0.1412	0.5171	0.411	-0.0204	-0.2731	-0.5166	0.065	0.4172	0.3027	0.377	-0.0441	0.0252	0.647	0.1094	0.6051	58.0723	25.6608	24.2882
3	4.496	-1.332	1.1359	3.7204	-2.0617	2.681	0.2044	1.202	0.1062	-1.1357	-0.1125	-0.3	0.8123	-0.0284	-0.0236	0.4464	0.0201	0.1925	0.8677	-0.0381	0.5361	53.5117	18.6725	15.5251
4	5.7561	-0.4665	2.2068	1.966	0.2062	1.9723	-0.0379	0.0782	0.47	-0.2577	0.0508	-0.1684	0.504	-0.2693	0.0081	0.3634	-0.0732	0.116	0.6761	0.1317	0.4889	44.7111	22.0756	22.5339
5	2.2475	-0.3178	2.31	0.8963	0.8433	5.553	-0.3988	-0.1399	0.635	-0.0973	-0.286	0.2868	-0.1951	-0.2701	-0.3342	0.3557	-0.1219	0.1586	0.9457	0.1191	0.3848	32.3295	28.1759	19.2427
6	1.7098	0.9428	1.5871	0.4121	0.733	1.3556	0.0952	-0.1788	0.0271	0.2362	-0.1466	0.1375	0.7265	-0.2334	0.1369	0.5642	0.0299	0.089	0.4274	0.0484	0.586	3.692	38.3919	52.3403
7	3.9318	0.0463	-0.038	1.387	0.3411	3.8409	-0.0052	-0.0153	0.5198	0.0113	0.158	0.2199	-0.0785	-0.5156	-0.1465	0.4061	-0.0046	0.0242	0.3511	0.0601	0.5743	-2.2103	45.1809	34.4668
8	1.2311	-0.3623	-1.4361	1.2828	0.4362	3.8282	-0.1375	-0.061	0.3196	-0.0719	0.0445	0.2954	-0.6683	0.5528	0.0547	0.4873	-0.1326	0.0044	0.5596	0.0452	0.5414	10.2966	49.5028	25.251
9	4.0264	1.4289	2.184	0.2746	0.5004	1.2739	-0.0953	0.7138	-1.3787	0.0215	0.7576	-0.3638	-0.2122	1.1334	-0.5894	0.7137	0.0688	0.2193	0.7244	-0.1868	0.9699	58.4839	57.8267	40.0765
10	2.5383	0.8885	-2.2576	4.2585	-1.6835	4.6841	-0.2683	-0.3445	-0.6793	0.0075	-0.2038	-0.4656	0.332	0.6301	0.3722	0.4924	-0.0874	0.012	0.6997	0.1583	0.8463	59.4626	63.5925	58.2874
11	1.4712	1.0436	-1.589	1.296	-0.422	3.8504	0.1201	-0.1572	-0.2606	0.2389	-0.1468	-0.2779	-0.2305	0.2162	-0.1102	0.5188	-0.1368	0.0008	0.6995	0.1579	0.7498	49.6003	60.1983	65.3082
12	0.9422	0.3455	-1.0248	0.6814	0.5722	2.6704	-0.2729	0.0048	-0.3136	-0.023	-0.0908	-0.2143	0.0846	-0.404	-0.0816	0.8545	-0.3327	-0.1541	1.007	0.2529	0.7638	44.8461	50.4509	74.4594
13	-0.0709	0.0422	0.2126	-0.1092	-0.0265	1.4883	-0.2035	-0.1764	0.2269	-0.3746	-0.1682	0.5617	-0.731	-0.5795	0.416	0.752	0.1543	-0.2139	1.0153	-0.2069	0.8537	9.9721	24.3832	59.4738
14	2.1185	0.4431	0.5489	2.1664	1.9083	5.8386	0.0714	-0.5425	0.1976	0.2607	-0.5775	0.4418	0.2381	-0.9991	0.3457	0.4669	-0.0918	0.0173	0.7751	-0.0703	0.5543	16.6426	20.6172	75.4489
15	3.6728	-0.5381	3.1077	0.3929	-1.244	4.4634	1.1049	-0.7475	-0.2495	0.4901	-0.427	0.4102	1.9393	-0.9339	0.8825	0.6569	-0.2734	0.0767	0.6479	0.0554	0.6315	20.2701	11.2867	76.8193
16	3.0172	0.1609	1.2919	1.7503	0.3624	0.7654	-0.0937	0.3611	-0.0545	0.1866	-0.0417	0.0994	0.0132	0.5007	0.0329	0.5246	-0.1127	0.0578	0.6583	0.031	0.372	37.3037	23.1857	80.3769
17	0.1548	-0.4164	0.1777	0.6245	-0.0706	0.4452	-0.1554	-0.0394	0.1733	0.0493	-0.8978	-0.7954	1.1164	1.6391	0.8376	0.8901	0.1447	0.1205	0.9336	0.3457	0.9084	30.9285	7.1992	47.1733
18	1.998	0.1596	0.2451	3.035	-3.3779	7.1716	-0.2334	0.062	-0.3172	-0.9566	-0.2252	0.0146	1.998	-0.299	0.3547	0.9063	-0.0326	0.1247	0.3585	-0.0012	0.622	18.5671	8.0543	32.8948
19	2.1351	0.6091	-0.8044	2.7507	-3.808	8.8827	-0.4198	0.3192	-0.1615	-0.2215	-0.0309	-0.0071	0.6644	-0.0668	0.2932	0.4612	-0.0747	-0.0246	0.4485	-0.0069	0.5079	15.7866	22.7472	23.034
20	0.021	-0.0227	0.0009	0.019	-0.0069	0.026	-0.3057	-0.267	0.1687	0.3611	0.131	0.1546	-0.7839	0.0656	0.0283	1.6589	0.3673	-0.1858	1.3823	-0.0043	1.1097	8.7183	27.6254	41.4416
21	2.5163	-0.2383	1.1658	2.7777	-0.8465	0.7477	-0.2313	0.4535	0.5961	0.6325	-0.2719	-0.251	-0.636	0.4563	0.4107	0.541	-0.0492	-0.1189	0.4782	0.0112	0.4054	15.464	31.0986	21.2256
22	0.3701	0.6502	0.8601	0.6487	0.428	1.9169	-0.2372	0.2434	0.4076	0.0017	-0.2488	-0.1564	-0.2684	0.2101	0.6729	0.9405	0.024	-0.1577	0.5709	0.0628	0.9844	19.2127	64.412	54.1469
23	2.9697	-1.1427	2.3513	1.6628	-1.0197	3.8127	-0.7751	-0.5017	0.9128	0.6006	0.0455	-0.0697	-0.8739	-0.5707	0.6732	0.8571	0.0804	-0.0898	0.5145	-0.1178	0.865	20.3396	60.9755	74.193
24	3.4227	-1.9717	2.609	1.9643	-1.5708	3.4474	0.3118	-0.0584	0.1726	-0.1851	-0.3151	0.1596	0.3841	-0.1325	0.0119	0.7219	-0.0319	0.0108	0.4272	-0.0495	0.4712	25.7674	46.2817	77.9619
25	0.8969	-0.3	1.2164	0.0815	-0.4067	4.2525	-0.0496	-0.3727	-0.0511	-0.0295	-0.0685	0.1166	0.1148	-0.6126	0.3147	0.7401	-0.0186	-0.0487	0.4868	-0.0002	0.6723	29.5248	68.8079	41.067
26	1.6345	-0.1141	0.7227	2.5976	2.2195	4.3752	-0.3912	0.0485	0.6034	-0.5887	-0.0561	0.1737	-1.4275	0.2774	0.2213	1.0835	-0.2555	-0.0942	0.5782	0.0712	0.7431	29.3763	69.274	24.0877
27	0.1838	0.1686	-0.3642	2.2101	0.9128	1.4378	-0.0127	-0.0635	0.4904	-0.539	0.4167	-0.6978	-1.3652	0.9284	1.1539	1.3585	-0.9938	-0.0598	0.6039	0.162	0.8309	37.9299	71.1242	19.5791
28	1.0478	0.8506	0.7557	2.4282	3.1048	3.9358	-0.0376	0.3084	0.1268	-0.0167	0.303	-0.324	-0.1414	0.831	-0.1647	0.7323	-0.2613	-0.0387	0.7336	0.0575	0.6016	32.5503	52.2147	11.7442
29	0.0333	0.1551	0.6028	0.721	-0.9956	1.8105	-0.1363	0.0485	-0.0684	0.1059	-0.0898	0.2491	0.7009	-0.3334	0.0553	0.5739	-0.0209	0.0279	0.6098	-0.1313	0.5087	46.3675	8.1444	51.6284
30	1.7948	-0.3835	0.0854	3.875	2.9349	6.2504	-0.0685	-0.1533	-0.1721	0.4584	-0.0248	-0.1341	0.5021	0.5093	0.0328	0.5058	0.0655	0.0573	0.4833	0.0525	0.4425	58.8912	9.7664	65.3343
31	1.0632	-0.7601	-1.527	0.8407	2.1634	5.794	-0.2188	-0.1827	-0.0385	0.1937	0.1414	0.1473	-0.3123	-0.0347	-0.0407	0.6596	0.0247	0.0198	0.4984	0.0398	0.3983	55.7053	21.8567	74.2179
32	3.3172	0.4165	-2.1647	2.249	2.5678	6.7419	0.1813	-0.202	0.3157	-0.3145	0.0914	-0.2396	-0.9539	0.5424	-0.3859	0.6626	-0.1191	0.0485	0.6099	0.0089	0.5057	60.0174	30.059	76.4485

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 54 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 55 through 113 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 114 through 145 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 146 through 212 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 213 through 243 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 8 through 54 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 55 through 145 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 146 through 242 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 8 through 54 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 55 through 145 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 146 through 212 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 213 through 243 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 8 through 53 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 54 through 113 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 114 through 160 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 161 through 245 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 8 through 53 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 54 through 160 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 161 through 207 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 208 through 212 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 213 through 244 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 8 through 53 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 54 through 145 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 146 through 242 )
25	X-RAY DIFFRACTION	25	chain 'G' and (resid 8 through 54 )
26	X-RAY DIFFRACTION	26	chain 'G' and (resid 55 through 113 )
27	X-RAY DIFFRACTION	27	chain 'G' and (resid 114 through 160 )
28	X-RAY DIFFRACTION	28	chain 'G' and (resid 161 through 242 )
29	X-RAY DIFFRACTION	29	chain 'H' and (resid 8 through 54 )
30	X-RAY DIFFRACTION	30	chain 'H' and (resid 55 through 160 )
31	X-RAY DIFFRACTION	31	chain 'H' and (resid 161 through 185 )
32	X-RAY DIFFRACTION	32	chain 'H' and (resid 186 through 242 )

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