PDB-2yn0: tau55 histidine phosphatase domain

ID or keywords:

Entry

Database: PDB / ID: 2yn0

Title

tau55 histidine phosphatase domain

Components

TRANSCRIPTION FACTOR TAU 55 KDA SUBUNIT

Keywords

TRANSCRIPTION /

RNA POLYMERASE III

Function / homology

Function and homology information

5S class rRNA transcription by RNA polymerase III / transcription factor TFIIIC complex /

transcription initiation at RNA polymerase III promoter /

phosphatase activity / transcription by RNA polymerase III /

DNA binding /

nucleus
Similarity search - Function

Biological species

SACCHAROMYCES CEREVISIAE (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 1.5 Å

Authors

Taylor, N.M.I. / Glatt, S. / Hennrich, M. / von Scheven, G. / Grotsch, H. / Fernandez-Tornero, C. / Rybin, V. / Gavin, A.C. / Kolb, P. / Muller, C.W.

Citation

Journal: J.Biol.Chem. / Year: 2013
Title: Structural and Functional Characterization of a Phosphatase Domain within Yeast General Transcription Factor Iiic.
Authors: Taylor, N.M.I. / Glatt, S. / Hennrich, M.L. / Von Scheven, G. / Grotsch, H. / Fernandez-Tornero, C. / Rybin, V. / Gavin, A.C. / Kolb, P. / Muller, C.W.

History

Deposition	Oct 11, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 3, 2013	Provider: repository / Type: Initial release
Revision 1.1	Apr 17, 2013	Group: Database references
Revision 1.2	Jun 12, 2013	Group: Database references
Revision 1.3	Apr 3, 2019	Group: Data collection / Other / Source and taxonomy Category: entity_src_gen / pdbx_database_proc / pdbx_database_status Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 2.0	May 8, 2024	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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	2yn0.cif.gz	165.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2yn0.ent.gz	135.4 KB	Display	PDB format
PDBx/mmJSON format	2yn0.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/yn/2yn0 ftp://data.pdbj.org/pub/pdb/validation_reports/yn/2yn0	HTTPS FTP

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Related structure data

Related structure data	2yn2C C: citing same article (ref.)
Similar structure data	5o85-1 5ewo-d 5lub-1 1yu6-1 4y6n-d 6yw3-d 5fbg-1 3igs-1 1pl9-d 4fek-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	#257 - May 2021 Fetal Hemoglobin similarity (4) #50 - Feb 2004 Glycolytic Enzymes similarity (4) #225 - Sep 2018 Phytase similarity (1)

Deposited unit

A: TRANSCRIPTION FACTOR TAU 55 KDA SUBUNIT

hetero molecules

31.1 kDa, 1 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)	80.580, 86.730, 44.310
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-2046- HOH

#1: Protein	TRANSCRIPTION FACTOR TAU 55 KDA SUBUNIT / TFIIIC 55 KDA SUBUNIT / TRANSCRIPTION FACTOR C SUBUNIT 7 / TAU55 Mass: 31047.025 Da / Num. of mol.: 1 / Fragment: HISTIDINE PHOSPHATASE DOMAIN, RESIDUES 1-272 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q12415
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.5 Å³/Da / Density % sol: 50.75 % / Description: NONE
Crystal grow	Details: 0.77 M NAH2PO4, 1.23 M K2HPO4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.00849
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 24, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00849 Å / Relative weight: 1
Reflection	Resolution: 1.5→50 Å / Num. obs: 50268 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 4.05 % / B_iso Wilson estimate: 15.411 Å² / R_merge(I) obs: 0.16 / Net I/σ(I): 15.5
Reflection shell	Resolution: 1.5→1.54 Å / Redundancy: 4.02 % / R_merge(I) obs: 0.99 / Mean I/σ(I) obs: 2.19 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
SHARP		phasing

Refinement

Method to determine structure:

SIRAS
Starting model: NONE

Resolution: 1.5→43.365 Å / SU ML: 0.16 / σ(F): 1.78 / Phase error: 17.15 / Stereochemistry target values: ML
Details: RESIDUES 2-260 ARE VISIBLE IN THE ELECTRON DENSITY, EXCEPT FOR RESIDUES 216-225 WHICH ARE DISORDERED

	R_factor	Num. reflection	% reflection
R_free	0.1826	2551	5.1 %
R_work	0.1559	-	-
obs	0.1573	50251	99.44 %

Solvent computation

Shrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 45.494 Å² / k_sol: 0.46 e/Å³

Displacement parameters

B_iso mean: 20.35 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.6438 Å²	0 Å²	0 Å²
2-	-	-1.6942 Å²	0 Å²
3-	-	-	7.338 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→43.365 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2013	0	5	293	2311

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2161
X-RAY DIFFRACTION	f_angle_d	1.248	2960
X-RAY DIFFRACTION	f_dihedral_angle_d	13.444	833
X-RAY DIFFRACTION	f_chiral_restr	0.079	313
X-RAY DIFFRACTION	f_plane_restr	0.007	384

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 (%)
1.5-1.5536	0.2823	274	0.2667	4694	X-RAY DIFFRACTION	100
1.5536-1.6158	0.2452	277	0.2367	4688	X-RAY DIFFRACTION	100
1.6158-1.6894	0.2397	266	0.2102	4702	X-RAY DIFFRACTION	100
1.6894-1.7785	0.2265	246	0.1833	4751	X-RAY DIFFRACTION	100
1.7785-1.8899	0.1843	230	0.1585	4752	X-RAY DIFFRACTION	100
1.8899-2.0358	0.1624	240	0.1372	4780	X-RAY DIFFRACTION	100
2.0358-2.2407	0.164	281	0.1342	4755	X-RAY DIFFRACTION	100
2.2407-2.5649	0.1767	243	0.1381	4790	X-RAY DIFFRACTION	100
2.5649-3.2313	0.1648	252	0.1373	4825	X-RAY DIFFRACTION	99
3.2313-43.3831	0.1657	242	0.1495	4963	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	0.2158	-0.1712	0.137	0.5731	0.0658	0.1086	0.0291	-0.0386	-0.0032	0.0037	-0.0214	-0.0862	0.0125	0.0622	0	0.0886	0.0053	-0.0013	0.1006	0.0006	0.0863	32.9499	11.4417	40.7012
2	0.006	-0.0055	-0.0017	0.0047	0.0026	0.0198	0.0033	-0.2383	0.052	0.0717	0.0454	-0.2128	-0.0434	0.1124	0.0001	0.1533	0.0073	-0.0192	0.1589	-0.0161	0.1027	31.449	15.1412	51.8378
3	0.0168	-0.0242	-0.0081	0.1405	0.1392	0.1512	-0.0634	-0.1217	0.0612	-0.0079	-0.0748	0.0554	-0.0078	-0.0788	-0.2097	0.0962	0.0291	0.0117	0.1758	-0.0141	0.0424	20.1729	15.7561	56.7089
4	0.6179	-0.2058	0.1397	0.2315	-0.1115	0.0977	0.0231	0.0223	-0.1409	0.0371	-0.0244	0.0078	0.033	0.0463	0.003	0.1071	0.0021	0.0008	0.0873	0.0163	0.073	22.7627	6.077	44.5845
5	0.0174	-0.0057	-0.0003	0.0511	-0.0069	0.0007	0.0589	0.3017	0.1622	-0.0306	-0.0227	-0.0725	-0.1084	0.0873	0.0028	0.2608	0.0745	-0.0234	0.4801	0.0276	0.0401	29	10.7703	21.7452
6	0.1247	-0.0318	0.0718	0.0077	-0.0164	0.038	0.0174	0.2522	-0.3483	-0.0519	-0.1372	-0.1572	0.13	0.0065	0	0.1669	0.0349	-0.0013	0.1789	-0.0324	0.1829	28.436	-0.8801	34.439
7	0.0072	-0.0064	-0.0049	0.0055	0.0047	0.0087	0.0736	0.0649	-0.1365	0.0186	0.0177	0.058	-0.0189	0.0951	0.0001	0.1505	0.0227	-0.0025	0.1089	0.0311	0.1824	31.4079	-3.008	45.5345
8	0.0052	0.0144	-0.0087	0.051	-0.0567	0.051	0.0717	0.036	-0.4778	0.0068	-0.0225	0.1805	0.0484	0.0929	0	0.169	0.0074	-0.02	0.1222	0.0372	0.2567	19.6084	-3.6742	45.8253
9	0.0036	-0.0004	0.0037	0.0013	-0.0012	0.0037	0.0726	0.1478	-0.2642	-0.0284	-0.0767	0.1558	-0.0211	-0.095	-0	0.1699	0.0011	-0.0187	0.1685	-0.0631	0.2023	15.9455	1.7589	32.4664
10	0.0104	0.003	0.0012	0.0063	0.0052	0.0039	0.0031	0.0129	-0.1263	-0.0697	-0.0274	-0.0056	0.0499	-0.0807	-0	0.2181	0.1085	-0.0165	0.3401	-0.0318	0.1087	22.4866	3.2354	23.1476
11	0.0836	-0.0206	0.0193	0.0848	0.0106	0.1469	0.118	0.2101	0.0162	0.0255	-0.1136	0.0985	0.0994	0.0622	-0.067	0.1402	0.0552	-0.017	0.2024	-0.0072	0.0551	15.0772	12.7717	25.9843
12	0.0201	0.0172	0.0007	0.0147	-0.0023	0.0242	0.1015	0.0523	-0.0481	-0.0703	-0.0152	0.0905	0.0436	0.0553	0	0.1265	0.0034	-0.0218	0.1271	-0.0144	0.1232	9.5823	9.3092	33.6355
13	0.1762	0.1082	-0.1109	0.0601	-0.0758	0.3376	-0.0107	0.1121	-0.3231	0.1198	0.0172	-0.0644	-0.0753	-0.0203	0.002	0.1146	-0.0303	-0.0103	0.0969	0.0017	0.2196	6.5568	1.9836	42.5204
14	0.1708	0.0597	0.1881	0.5193	0.4808	0.5208	-0.0179	0.0313	0.0129	-0.0565	-0.0543	0.1381	0.0015	0.0065	-0.2561	0.089	0.0048	-0.0014	0.0877	0.0171	0.093	13.4348	17.1723	37.8309
15	0.0249	-0.0115	-0.0088	0.0309	0.0159	0.0074	-0.0227	-0.1325	0.0023	-0.2079	-0.0946	0.1523	-0.2812	0.1342	-0.0004	0.2119	-0.0078	-0.0623	0.0986	-0.0004	0.2129	13.4274	32.7573	36.5808
16	0.0629	-0.0487	0.0833	0.0352	-0.0618	0.099	-0.0501	0.0022	0.1777	0.0209	0.0208	0.0715	0.0336	-0.0098	-0	0.088	0.001	0.0017	0.1003	0.0043	0.137	16.9708	19.9453	44.1331
17	0.0039	-0.0023	0.0045	0.0039	0.0005	0.0053	-0.0405	0.011	-0.295	0.2024	0.1583	0.0828	-0.0697	0.1857	-0.0001	0.1496	0.0149	-0.0182	0.1554	0.0104	0.2356	-3.2497	18.6593	48.6523
18	0.0191	0.0138	-0.0138	0.0105	-0.0097	0.0064	-0.2589	0.3188	-0.3381	0.1076	0.2323	-0.1812	0.2003	-0.3171	-0.0001	0.2449	0.0052	0.0112	0.1983	-0.0147	0.3344	-6.3678	13.8805	52.9716
19	0.3643	-0.4801	-0.0413	0.6329	0.0406	0.0034	-0.0262	-0.0234	0.1641	0.0034	0.0034	0.1298	-0.0075	0.0228	-0	0.1053	-0.0005	-0.0037	0.1015	0.0024	0.1504	15.0605	19.5746	43.9687
20	0.0014	0.0032	-0.0053	0.0053	-0.0087	0.0141	-0.0986	-0.0273	0.0839	-0.2117	-0.0185	0.0003	-0.2184	-0.0168	0.0003	0.262	-0.0593	-0.0768	0.2555	0.0668	0.1931	23.5285	23.9602	29.0504

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 3:41)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 42:45)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 46:57)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 58:94)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 95:99)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 100:111)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 112:115)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 116:124)
9	X-RAY DIFFRACTION	9	(CHAIN A AND RESID 125:129)
10	X-RAY DIFFRACTION	10	(CHAIN A AND RESID 130:133)
11	X-RAY DIFFRACTION	11	(CHAIN A AND RESID 134:143)
12	X-RAY DIFFRACTION	12	(CHAIN A AND RESID 144:147)
13	X-RAY DIFFRACTION	13	(CHAIN A AND RESID 148:159)
14	X-RAY DIFFRACTION	14	(CHAIN A AND RESID 160:191)
15	X-RAY DIFFRACTION	15	(CHAIN A AND RESID 192:196)
16	X-RAY DIFFRACTION	16	(CHAIN A AND RESID 197:209)
17	X-RAY DIFFRACTION	17	(CHAIN A AND RESID 210:213)
18	X-RAY DIFFRACTION	18	(CHAIN A AND RESID 214:227)
19	X-RAY DIFFRACTION	19	(CHAIN A AND RESID 228:255)
20	X-RAY DIFFRACTION	20	(CHAIN A AND RESID 256:260)

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