PDB-4bji: Sfc1-DBD

ID or keywords:

Entry

Database: PDB / ID: 4bji

Title

Sfc1-DBD

Components

TRANSCRIPTION FACTOR TAU SUBUNIT SFC1

Keywords

DNA BINDING PROTEIN

Function / homology

Function and homology information

RNA polymerase III cis-regulatory region sequence-specific DNA binding / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / transcription factor TFIIIC complex / RNA polymerase III general transcription initiation factor activity / transcription initiation at RNA polymerase III promoter / nucleus / cytosol / cytoplasm
Similarity search - Function

Biological species

SCHIZOSACCHAROMYCES POMBE (fission yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.45 Å

Authors

Taylor, N.M.I. / Baudin, F. / von Scheven, G. / Muller, C.W.

Citation

Journal: Nucleic Acids Res. / Year: 2013
Title: RNA Polymerase III-Specific General Transcription Factor Iiic Contains a Heterodimer Resembling Tfiif RAP30/RAP74.
Authors: Taylor, N.M.I. / Baudin, F. / Von Scheven, G. / Muller, C.W.

History

Deposition	Apr 18, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 31, 2013	Provider: repository / Type: Initial release
Revision 1.1	Aug 21, 2013	Group: Database references
Revision 1.2	Nov 6, 2013	Group: Database references
Revision 2.0	Nov 13, 2024	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4bji.cif.gz	141.9 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bj/4bji ftp://data.pdbj.org/pub/pdb/validation_reports/bj/4bji	HTTPS FTP

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Related structure data

Related structure data	4bjjC C: citing same article (ref.)
Similar structure data	1pxr-1 2psm-2 5m2q-2 1vjm-d 4wav-2 1fap-d 1s53-2 5vn9-1 6rnj-d 1e0p-d 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: TRANSCRIPTION FACTOR TAU SUBUNIT SFC1

25.2 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)	35.380, 67.640, 88.060
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	TRANSCRIPTION FACTOR TAU SUBUNIT SFC1 / TFIIIC SUBUNIT SFC1 / TRANSCRIPTION FACTOR C SUBUNIT 1 Mass: 25178.117 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN, RESIDUES 186-396 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast) Strain: 972 / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIPL / References: UniProt: O14229
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.12 Å³/Da / Density % sol: 41.89 % / Description: NONE
Crystal grow	pH: 8.5 Details: 0.2 M MAGNESIUM CHLORIDE, 0.1 M TRIS, PH 8.5, 20% PEG 3,350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.980062
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2009 Details: TWO CYLINDRICAL VERTICAL FOCUSING PARABOLIC MIRRORS
Radiation	Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.980062 Å / Relative weight: 1
Reflection	Resolution: 1.45→50 Å / Num. obs: 69358 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 3.01 % / B_iso Wilson estimate: 12.547 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 2.85
Reflection shell	Resolution: 1.45→1.49 Å / Redundancy: 1.74 % / R_merge(I) obs: 0.54 / Mean I/σ(I) obs: 2.85 / % possible all: 74

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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:

MAD
Starting model: NONE

Resolution: 1.45→44.03 Å / SU ML: 0.14 / σ(F): 1.91 / Phase error: 14.55 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1698	3492	5 %
R_work	0.1515	-	-
obs	0.1524	69339	95.77 %

Solvent computation

Shrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 51.475 Å² / k_sol: 0.454 e/Å³

Displacement parameters

B_iso mean: 19.21 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.03 Å²	0 Å²	0 Å²
2-	-	1.3471 Å²	0 Å²
3-	-	-	-1.3171 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→44.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1603	0	0	258	1861

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	1774
X-RAY DIFFRACTION	f_angle_d	1.339	2422
X-RAY DIFFRACTION	f_dihedral_angle_d	11.908	685
X-RAY DIFFRACTION	f_chiral_restr	0.078	268
X-RAY DIFFRACTION	f_plane_restr	0.008	307

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 (%)
1.4501-1.5019	0.2218	278	0.214	5200	X-RAY DIFFRACTION	75
1.5019-1.562	0.2071	351	0.1885	6047	X-RAY DIFFRACTION	89
1.562-1.6331	0.1847	348	0.169	6822	X-RAY DIFFRACTION	99
1.6331-1.7192	0.1615	365	0.1434	6827	X-RAY DIFFRACTION	100
1.7192-1.827	0.1575	375	0.1398	6859	X-RAY DIFFRACTION	100
1.827-1.968	0.1638	351	0.1362	6860	X-RAY DIFFRACTION	100
1.968-2.1661	0.1632	338	0.1396	6826	X-RAY DIFFRACTION	99
2.1661-2.4795	0.1491	375	0.1383	6808	X-RAY DIFFRACTION	99
2.4795-3.1238	0.1745	365	0.1519	6812	X-RAY DIFFRACTION	99
3.1238-44.0503	0.1719	346	0.1566	6786	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	0.0255	0.0133	0.0118	0.0147	0.0123	0.0033	0.1374	-0.2301	0.3318	0.0901	-0.0412	-0.1607	-0.1391	0.2869	0.0007	0.1314	-0.1088	-0.012	0.3557	-0.1085	0.1797	43.8837	63.2234	30.2068
2	0.1705	0.0712	-0.2055	0.1518	0.144	0.4562	0.0526	-0.0722	-0.0304	0.022	0.1699	-0.0239	0.0605	0.4396	0.0664	0.0384	0.0292	-0.0261	0.1733	-0.0132	0.0821	42.8943	53.9287	19.592
3	0.0739	-0.0016	-0.0402	0.0048	0.0012	0.0222	0.0611	0.0776	0.0529	0.0262	0.0788	-0.1511	-0.0767	0.1182	0.0002	0.1647	0.0347	-0.0502	0.5999	-0.0855	0.1444	46.7087	56.8568	33.805
4	0.006	-0.0112	0.0032	0.0127	-0.0045	0.0006	-0.139	-0.0033	-0.0148	0.2727	-0.1135	0.0159	-0.046	0.3903	0	0.2014	-0.0193	-0.0491	0.2989	0.0132	0.1556	37.229	56.4236	42.3701
5	0.049	-0.0223	-0.0418	0.1036	-0.1419	0.1551	-0.0364	-0.0553	-0.0064	0.1821	-0.0465	0.0203	0.1466	0.098	-0.0393	0.1498	-0.0395	0.0055	0.1038	0.0015	0.0626	29.0025	54.2662	34.4738
6	0.0631	0.0012	-0.0367	0.0329	-0.0497	0.1165	0.0046	-0.0709	0.0424	0.0264	-0.0737	-0.0197	-0.0396	-0.1194	0	0.0922	-0.0186	-0.0017	0.0654	-0.0198	0.0689	26.2605	57.9505	22.9987
7	-0.0026	-0.015	0.0056	0.0131	-0.0033	0.0248	-0.0071	-0.3276	0.0092	0.262	0.1633	-0.0501	-0.3046	-0.0267	-0.0001	0.1324	0.022	0.0126	0.1808	-0.0203	0.0912	22.4723	61.4816	29.0482
8	0.032	-0.0026	0.0124	-0.0034	-0.0071	0.0034	-0.3717	-0.0178	0.1282	0.2821	-0.2845	-0.2355	-0.2715	-0.1096	-0.0002	0.4352	0.1091	-0.0938	0.2104	-0.1092	0.2243	26.1932	65.8872	35.1436
9	0.2703	-0.3149	0.2234	0.0666	-0.1428	0.4958	-0.0288	-0.0241	0.012	0.0665	0.0056	-0.068	-0.0873	0.2901	-0	0.08	-0.0245	-0.0136	0.077	-0.0012	0.0484	35.0488	57.0412	22.2888
10	0.0607	-0.009	0.0473	0.0226	0.0538	0.1401	0.0533	0.0203	-0.074	0.0348	-0.0821	-0.078	0.0145	-0.0802	-0	0.0623	-0.0076	-0.0039	0.0502	-0.0142	0.0879	28.5055	51.0341	12.2185
11	0.0148	0.0225	-0.0148	0.0627	-0.0013	0.0162	-0.0161	0.0632	0.3028	-0.1381	-0.1171	-0.2197	-0.0502	0.2327	-0.0004	0.1158	-0.0294	-0.0038	0.0695	0.0159	0.2323	28.276	69.3854	10.6591
12	0.0099	-0.0123	-0.006	0.0139	-0.0051	0.0091	-0.3394	-0.2711	0.0483	0.2314	0.116	-0.0411	-0.0656	-0.1008	0.0001	0.269	-0.1147	-0.1122	0.2739	0.0575	0.6877	22.1102	76.2556	15.936
13	0.0154	0.0121	0.0284	0.0465	0.0238	0.0598	-0.2099	-0.0952	0.2167	0.172	0.0927	-0.1223	-0.1514	-0.2325	-0.0034	0.1318	0.051	-0.0275	0.1237	-0.0507	0.107	18.8294	66.0784	21.4775
14	0.0284	-0.0269	-0.0326	0.0643	0.0284	0.0059	-0.3136	-0.3666	-0.0212	0.3489	0.311	0.1104	-0.0751	-0.4219	-0.0083	0.1395	0.0916	-0.0062	0.1096	-0.0523	0.1057	13.9994	70.7812	15.0108
15	0.3994	-0.2209	-0.1939	0.1812	-0.05	0.2294	-0.0218	-0.0412	0.0771	0.0009	0.0066	-0.0043	-0.018	-0.1467	-0	0.0549	0.0137	-0.0058	0.0576	-0.026	0.0801	19.313	62.0975	11.6854
16	0.0893	0.0245	0.0617	0.031	0.0283	0.0638	0.056	0.3565	-0.3501	0.3243	-0.0911	-0.0216	0.0392	-0.0961	0.0171	0.0624	-0.0075	0.012	0.094	-0.0339	0.0855	19.6873	50.747	2.3689
17	0.3374	-0.196	-0.1738	0.0967	-0.2053	0.2934	0.0182	0.1258	0.0648	0.0203	-0.0013	-0.0442	-0.0454	0.0457	-0	0.0449	-0.0043	-0.002	0.0508	-0.0088	0.0674	28.4115	58.6702	2.8098
18	0.0225	0.0115	-0.0029	0.0091	0.0117	0.0159	0.1158	0.2469	0.3547	-0.5971	0.0322	-0.2963	-0.193	-0.2804	0.0014	0.1542	0.0355	0.0866	0.0719	0.0237	0.2176	19.3743	72.0017	6.1498
19	0.0369	-0.0029	-0.1447	0.1338	-0.1077	0.7219	0.1279	0.0604	0.1478	-0.0513	0.2765	-0.3908	-0.4719	-0.442	0.0318	0.191	0.0952	0.0646	0.1185	0.0283	0.2424	13.7045	76.403	9.9182
20	0.0125	-0.0597	0.0489	0.0954	-0.0983	0.0288	-0.0427	0.2549	-0.0032	-0.2279	0.0237	0.1078	-0.056	-0.1991	-0	0.1421	-0.0072	0.0098	0.1641	0.0286	0.1105	14.6093	67.6377	-3.4533

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 190:193)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 194:208)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 209:212)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 213:216)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 217:230)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 231:238)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 239:245)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 246:250)
9	X-RAY DIFFRACTION	9	(CHAIN A AND RESID 251:280)
10	X-RAY DIFFRACTION	10	(CHAIN A AND RESID 281:290)
11	X-RAY DIFFRACTION	11	(CHAIN A AND RESID 291:294)
12	X-RAY DIFFRACTION	12	(CHAIN A AND RESID 295:304)
13	X-RAY DIFFRACTION	13	(CHAIN A AND RESID 305:308)
14	X-RAY DIFFRACTION	14	(CHAIN A AND RESID 309:316)
15	X-RAY DIFFRACTION	15	(CHAIN A AND RESID 317:335)
16	X-RAY DIFFRACTION	16	(CHAIN A AND RESID 336:339)
17	X-RAY DIFFRACTION	17	(CHAIN A AND RESID 340:363)
18	X-RAY DIFFRACTION	18	(CHAIN A AND RESID 364:367)
19	X-RAY DIFFRACTION	19	(CHAIN A AND RESID 368:376)
20	X-RAY DIFFRACTION	20	(CHAIN A AND RESID 377:390)

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