PDB-3psj: Crystal Structure of the Spt6 Tandem SH2 Domain from Saccharomyce...

ID or keywords:

Entry

Database: PDB / ID: 3psj

Title

Crystal Structure of the Spt6 Tandem SH2 Domain from Saccharomyces cerevisiae, Form Se-Spt6 (1247-1451)

Components

Transcription elongation factor SPT6

Keywords

TRANSCRIPTION / Tandem SH2 / Transcription Elongation / Nucleus

Function / homology

Function and homology information

carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / regulation of transcriptional start site selection at RNA polymerase II promoter / transcription antitermination factor activity, DNA binding / regulation of mRNA 3'-end processing / nucleosome organization / poly(A)+ mRNA export from nucleus / transcription elongation-coupled chromatin remodeling / nucleosome binding / transcription elongation factor complex / transcription antitermination ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.702 Å

Authors

Close, D. / Hill, C.P.

Citation

Journal: J.Mol.Biol. / Year: 2011
Title: Crystal structures of the S. cerevisiae Spt6 core and C-terminal tandem SH2 domain.
Authors: Close, D. / Johnson, S.J. / Sdano, M.A. / McDonald, S.M. / Robinson, H. / Formosa, T. / Hill, C.P.

History

Deposition	Dec 1, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 30, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Aug 3, 2011	Group: Database references
Revision 1.3	Nov 8, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3psj.cif.gz	126.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3psj.ent.gz	108.5 KB	Display	PDB format
PDBx/mmJSON format	3psj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3psj_validation.pdf.gz	443 KB	Display	wwPDB validaton report
Full document	3psj_full_validation.pdf.gz	444.4 KB	Display
Data in XML	3psj_validation.xml.gz	9.4 KB	Display
Data in CIF	3psj_validation.cif.gz	11.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ps/3psj ftp://data.pdbj.org/pub/pdb/validation_reports/ps/3psj	HTTPS FTP

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Related structure data

Related structure data	3psfC 3psiC 3pskC C: citing same article (ref.)
Similar structure data	3psk-4 2zg7-d 5ufi-3 5j9v-d 2z5r-d 2lm5-d 2v70-4 6ts0-d 6wyf-d 6gkb-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
Related items in Molecule of the Month	#55 - Jul 2004 DNA Ligase similarity (1)

Deposited unit

A: Transcription elongation factor SPT6

hetero molecules

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)	98.247, 98.247, 131.927
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	98
Space group name H-M	I4₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-12- HOH

#1: Protein	Transcription elongation factor SPT6 / Chromatin elongation factor SPT6 Mass: 25149.062 Da / Num. of mol.: 1 / Fragment: unp residues 1247-1451 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288C / Gene: CRE2, G6169, SPT6, SSN20, YGR116W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P23615
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.16 Å³/Da / Density % sol: 61.13 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 22% PEG 4000, 0.3M Ammonium Sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-1 / Wavelength: 0.97908 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2008

Radiation

Monochromator: Side-scattering cuberoot I-beam bent single crystal; asymetric cut 12.2 degs.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97908 Å / Relative weight: 1

Reflection

Redundancy: 6.9 % / Av σ(I) over netI: 25.1 / Number: 108109 / R_merge(I) obs: 0.07 / Χ²: 1 / D res high: 2.7 Å / D res low: 35 Å / Num. obs: 15594 / % possible obs: 92.2

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.81	35	93.5	1	0.038	0.867	8.1
4.61	5.81	95	1	0.057	0.98	8.1
4.03	4.61	95.5	1	0.056	0.991	8
3.66	4.03	96	1	0.073	1.052	8.1
3.4	3.66	96	1	0.099	1.005	8
3.2	3.4	96.2	1	0.14	0.993	7.7
3.04	3.2	95	1	0.202	1.047	7
2.91	3.04	92.8	1	0.267	1.103	5.6
2.8	2.91	87	1	0.29	1.086	4.3
2.7	2.8	74.5	1	0.296	1.028	3.5

Reflection

Resolution: 2.7→35 Å / Num. obs: 15594 / % possible obs: 92.2 % / Redundancy: 6.9 % / R_merge(I) obs: 0.07 / Χ²: 1.005 / Net I/σ(I): 14.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.7-2.8	3.5	0.296	1259	1.028	1	74.5
2.8-2.91	4.3	0.29	1483	1.086	1	87
2.91-3.04	5.6	0.267	1540	1.103	1	92.8
3.04-3.2	7	0.202	1622	1.047	1	95
3.2-3.4	7.7	0.14	1630	0.993	1	96.2
3.4-3.66	8	0.099	1636	1.005	1	96
3.66-4.03	8.1	0.073	1601	1.052	1	96
4.03-4.61	8	0.056	1609	0.991	1	95.5
4.61-5.81	8.1	0.057	1626	0.98	1	95
5.81-35	8.1	0.038	1588	0.867	1	93.5

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.6.4_486	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.702→31.784 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.37 / σ(F): 0 / Phase error: 25.32 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2544	847	10.09 %	RANDOM
R_work	0.2067	-	-	-
obs	0.2116	8392	91.4 %	-
all	-	9239	-	-

Solvent computation

Shrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 44.395 Å² / k_sol: 0.39 e/Å³

Displacement parameters

B_iso max: 193.88 Å² / B_iso mean: 74.6976 Å² / B_iso min: 27.09 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.2791 Å²	-0 Å²	0 Å²
2-	-	-4.2791 Å²	-0 Å²
3-	-	-	8.5582 Å²

Refinement step

Cycle: LAST / Resolution: 2.702→31.784 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1589	0	5	31	1625

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	1632
X-RAY DIFFRACTION	f_angle_d	1.117	2206
X-RAY DIFFRACTION	f_chiral_restr	0.059	233
X-RAY DIFFRACTION	f_plane_restr	0.005	281
X-RAY DIFFRACTION	f_dihedral_angle_d	14.256	609

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.7021-2.8713	0.4096	125	0.3125	1045	1170	78
2.8713-3.0928	0.3209	140	0.2592	1256	1396	93
3.0928-3.4038	0.2884	137	0.2105	1288	1425	95
3.4038-3.8955	0.2746	143	0.2001	1291	1434	95
3.8955-4.905	0.1802	148	0.1553	1314	1462	95
4.905-31.7865	0.2518	154	0.2237	1351	1505	93

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	2.5495	-0.998	0.906	5.4527	0.5575	1.348	0.2146	-1.1051	-0.1194	0.9837	-0.3747	-0.5584	0.2814	-0.4196	0.154	0.6639	-0.2698	0.0336	0.6016	0.151	0.2589	36.0811	31.8746	62.1567
2	2.6515	0.0116	2.3114	6.5465	-0.6566	2.0943	0.1968	0.4884	0.6099	1.2329	-0.4995	1.7336	-1.984	0.3882	0.6726	0.7361	-0.148	0.1793	0.2616	-0.1122	0.5148	40.2412	44.3332	58.8139
3	5.0059	1.7883	-4.1209	4.1082	-0.9826	4.2306	0.4282	-1.7344	0.1317	0.8631	-0.2178	0.5281	-0.7591	2.0862	0.1679	0.3835	-0.2513	-0.0156	0.7026	0.0144	0.2287	50.0694	39.5348	59.9063
4	1.6474	-1.5737	0.654	2.076	0.2904	4.4935	0.1467	0.079	1.3352	-0.2714	-0.3182	-0.4727	-1.0742	-0.2497	0.0777	0.4626	-0.0196	0.0757	0.3505	0.0851	0.377	35.5887	34.0592	54.2237
5	4.9758	0.6127	3.4308	0.4629	0.7541	2.6126	-0.477	0.3942	0.9373	-0.4913	0.1855	-0.0772	-1.5457	1.0044	0.5051	0.3954	-0.198	0.0424	0.3935	-0.1067	0.2763	49.6931	40.962	52.4647
6	4.5316	1.4014	0.6573	3.2529	-0.2377	2.1072	1.0075	0.216	-0.356	0.6597	-0.2033	0.3662	0.2398	0.3499	-0.401	0.3776	0.0831	-0.003	0.269	0.0945	0.3408	35.809	31.7709	49.1603
7	2.6643	-1.4832	-0.3133	1.2856	-1.0279	3.1278	0.5459	-0.8128	-0.7174	-0.0531	-0.3026	0.3887	0.1816	0.3279	0.0674	0.2622	-0.1979	0.0051	0.3422	0.0003	0.4046	28.1769	22.881	53.07
8	2.0016	-6.0795	1.9873	6.677	-9.3307	1.9975	-0.8232	1.8689	0.3121	0.812	-1.5714	0.1818	-1.1466	1.2303	0.4883	0.5069	-0.0046	0.1053	0.4316	0.025	0.5194	39.3727	24.7822	42.9829
9	4.0037	1.8141	-0.9589	0.9278	-0.7687	2.6734	0.6344	0.0698	-1.4655	0.1746	-0.6389	-0.8134	0.3931	0.2069	-0.0598	0.3632	0.0861	-0.0732	0.3602	0.0531	0.5146	47.9614	25.9162	50.4622
10	1.9992	-0.6319	-4.8828	2.2271	-0.6979	3.4231	0.9446	2.5938	-2.3599	-0.1253	-1.1646	-0.1185	1.0031	-1.3485	0.6606	0.5753	-0.2106	0.0746	0.8177	0.2947	0.7081	63.3908	38.2601	43.4296
11	6.2864	-5.264	1.7219	2.0043	-5.9766	4.0552	-2.4728	-2.3337	0.7929	0.6882	0.7569	-2.1039	-0.6234	-0.5777	1.1247	0.4176	-0.1527	-0.0235	0.7117	-0.1114	0.5837	59.4119	51.1617	41.5647
12	3.9563	-1.485	0.7394	2.8138	1.3717	1.5756	-0.6807	1.4572	0.4471	-0.3449	0.6574	1.266	-0.0194	1.3335	0.37	0.3714	-0.0411	0.0824	0.7	0.3736	0.812	69.6778	50.6024	33.5084
13	4.2942	-0.7367	3.1949	4.7498	1.0501	3.0647	0.6469	-0.1992	0.2156	-0.2661	1.0413	-0.7223	0.768	-1.3475	-0.3952	0.7169	0.048	0.1703	0.7498	0.265	0.5018	68.8779	42.7503	30.1832
14	1.2701	0.05	0.7776	2.4471	0.4586	0.8429	-0.5141	-0.2308	0.1467	-0.7275	0.0722	0.7588	-0.1477	-0.7915	0.0443	0.4334	-0.1699	0.1854	0.2959	0.1868	0.322	53.1739	42.3224	40.7094
15	3.0248	1.5636	-1.1293	3.8194	-2.8837	2.3593	0.2492	-0.1756	0.2119	-0.6337	-0.9507	-0.9806	0.2612	-0.5923	0.9232	0.6065	-0.1242	0.2455	0.7778	-0.0618	0.7697	60.9069	46.6647	28.0148
16	2.5386	-2.6237	0.0217	3.9515	1.3566	2.6633	-0.3089	0.9291	-0.6445	0.1008	-0.9448	-0.3066	0.2305	0.4625	0.6622	0.4182	-0.0276	0.1972	0.3877	0.102	0.3496	51.0474	32.0531	39.9006
17	0.0659	0.1482	0.0543	0.3292	0.0951	0.0951	0.1917	-1.4062	0.4402	0.9636	-0.7885	0.0473	0.5693	-0.3956	0.2351	0.7952	0.03	-0.0008	0.3481	0.0701	0.725	51.2037	30.7542	31.3853
18	7.6266	3.6927	-2.1985	2.1642	-1.2305	5.0789	-0.3036	0.7131	-2.2464	-0.9773	-0.474	-1.1667	0.5093	-0.7527	0.4629	0.8866	0.2026	0.4931	0.4936	0.1328	0.9572	60.0049	30.0407	34.2496

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 1252:1263)	A	1252 - 1263
2	X-RAY DIFFRACTION	2	(chain A and resid 1264:1269)	A	1264 - 1269
3	X-RAY DIFFRACTION	3	(chain A and resid 1270:1277)	A	1270 - 1277
4	X-RAY DIFFRACTION	4	(chain A and resid 1278:1294)	A	1278 - 1294
5	X-RAY DIFFRACTION	5	(chain A and resid 1295:1303)	A	1295 - 1303
6	X-RAY DIFFRACTION	6	(chain A and resid 1304:1309)	A	1304 - 1309
7	X-RAY DIFFRACTION	7	(chain A and resid 1310:1323)	A	1310 - 1323
8	X-RAY DIFFRACTION	8	(chain A and resid 1324:1328)	A	1324 - 1328
9	X-RAY DIFFRACTION	9	(chain A and resid 1329:1349)	A	1329 - 1349
10	X-RAY DIFFRACTION	10	(chain A and resid 1350:1357)	A	1350 - 1357
11	X-RAY DIFFRACTION	11	(chain A and resid 1358:1366)	A	1358 - 1366
12	X-RAY DIFFRACTION	12	(chain A and resid 1367:1376)	A	1367 - 1376
13	X-RAY DIFFRACTION	13	(chain A and resid 1377:1381)	A	1377 - 1381
14	X-RAY DIFFRACTION	14	(chain A and resid 1382:1395)	A	1382 - 1395
15	X-RAY DIFFRACTION	15	(chain A and resid 1396:1408)	A	1396 - 1408
16	X-RAY DIFFRACTION	16	(chain A and resid 1409:1417)	A	1409 - 1417
17	X-RAY DIFFRACTION	17	(chain A and resid 1418:1422)	A	1418 - 1422
18	X-RAY DIFFRACTION	18	(chain A and resid 1423:1435)	A	1423 - 1435

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