PDB-5t8v: Chaetomium thermophilum cohesin loader SCC2, C-terminal fragment

ID or keywords:

Entry

Database: PDB / ID: 5t8v

Title

Chaetomium thermophilum cohesin loader SCC2, C-terminal fragment

Components

Putative uncharacterized protein

Keywords

CELL CYCLE / cohesin loader / heat repeats

Function / homology

Function and homology information

: / regulation of gene expression / chromatin binding / nucleus
Similarity search - Function

Biological species

Chaetomium thermophilum (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.798 Å

Model details

This C-terminal fragment of SCC2 extends from residue 385 to 1840.

Authors

Tomchick, D.R. / Yu, H. / Kikuchi, S. / Ouyang, Z. / Borek, D. / Otwinowski, Z.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Crystal structure of the cohesin loader Scc2 and insight into cohesinopathy.
Authors: Kikuchi, S. / Borek, D.M. / Otwinowski, Z. / Tomchick, D.R. / Yu, H.

History

Deposition	Sep 8, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 19, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 16, 2016	Group: Database references
Revision 1.2	Mar 6, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5t8v.cif.gz	759.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5t8v.ent.gz	638 KB	Display	PDB format
PDBx/mmJSON format	5t8v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5t8v_validation.pdf.gz	453.6 KB	Display	wwPDB validaton report
Full document	5t8v_full_validation.pdf.gz	461.3 KB	Display
Data in XML	5t8v_validation.xml.gz	42.4 KB	Display
Data in CIF	5t8v_validation.cif.gz	57.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t8/5t8v ftp://data.pdbj.org/pub/pdb/validation_reports/t8/5t8v	HTTPS FTP

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Related structure data

Similar structure data	4jhd-d 3euh-d 3aqp-d 2xnk-d 5jnx-d 5kmr-d 3rpu-2 5o7p-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: Putative uncharacterized protein

hetero molecules

163 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	66.733, 88.779, 160.296
Angle α, β, γ (deg.)	90.000, 93.170, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Putative uncharacterized protein Mass: 162400.016 Da / Num. of mol.: 1 / Fragment: SCC2 C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0032310 / Plasmid: pFastBacHT / Cell (production host): insect / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G0S557
#2: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇

#1: Protein

Putative uncharacterized protein

Mass: 162400.016 Da / Num. of mol.: 1 / Fragment: SCC2 C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0032310 / Plasmid: pFastBacHT / Cell (production host): insect / Cell line (production host): BTI-Tn-5B1-4 / Production host:

Trichoplusia ni (cabbage looper) / References: UniProt: G0S557

#2: Chemical

ChemComp-CIT / CITRIC ACID

Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.92 Å³/Da / Density % sol: 57.87 % / Mosaicity: 0.293 °
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 9% (w/v) PEG 6,000, 150 mM sodium citrate pH 5.2, 5 mM TCEP, 150 mM NaCl, 20 mM Tris pH 7.5, 15% ethylene glycol.

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97935 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2015 / Details: MONOCHROMATOR

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97935 Å / Relative weight: 1

Reflection

Resolution: 2.7→36.24 Å / Num. obs: 51321 / % possible obs: 99.8 % / Redundancy: 4.5 % / B_iso Wilson estimate: 44.64 Å² / R_merge(I) obs: 0.106 / R_pim(I) all: 0.057 / R_rim(I) all: 0.121 / Χ²: 0.934 / Net I/av σ(I): 15.196 / Net I/σ(I): 6.7 / Num. measured all: 229634

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	CC_1/2	Diffraction-ID	% possible all
2.7-2.75	3.8	1.103	0.448	1	97.9
2.75-2.8	4	0.98	0.561	1	99.1
2.8-2.85	4.2	0.873	0.574	1	99.4
2.85-2.91	4.3	0.813	0.64	1	99.9
2.91-2.97	4.4	0.709	0.73	1	100
2.97-3.04	4.5	0.641	0.762	1	100
3.04-3.12	4.6	0.529	0.833	1	100
3.12-3.2	4.6	0.41	0.889	1	100
3.2-3.3	4.6	0.319	0.926	1	100
3.3-3.4	4.6	0.245	0.954	1	100
3.4-3.52	4.6	0.217	0.957	1	100
3.52-3.66	4.6	0.155	0.978	1	100
3.66-3.83	4.6	0.119	0.986	1	100
3.83-4.03	4.6	0.094	0.991	1	100
4.03-4.29	4.6	0.069	0.994	1	100
4.29-4.62	4.6	0.059	0.996	1	100
4.62-5.08	4.6	0.058	0.995	1	100
5.08-5.81	4.5	0.061	0.995	1	100
5.81-7.32	4.4	0.048	0.997	1	100
7.32-36.24	4.4	0.029	0.999	1	99.1

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Phasing

Phasing	Method: SAD

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Processing

Software

Name	Version	Classification
HKL-3000		data scaling
MLPHARE		phasing
PHENIX	1.10.1_2155	refinement
PDB_EXTRACT	3.2	data extraction
HKL-3000		data reduction

Refinement

Method to determine structure:

SAD / Resolution: 2.798→36.24 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.36

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2673	2004	4.52 %	random
R_work	0.2275	-	-	-
obs	0.2293	44294	95.5 %	-

Solvent computation

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

Displacement parameters

B_iso max: 211.44 Å² / B_iso mean: 58.3625 Å² / B_iso min: 8.2 Å²

Refinement step

Cycle: final / Resolution: 2.798→36.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10314	0	18	0	10332
B_iso mean	-	-	98.91	-	-
Num. residues	-	-	-	-	1315

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	10477
X-RAY DIFFRACTION	f_angle_d	0.488	14164
X-RAY DIFFRACTION	f_chiral_restr	0.036	1686
X-RAY DIFFRACTION	f_plane_restr	0.003	1799
X-RAY DIFFRACTION	f_dihedral_angle_d	13.436	6492

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.7982-2.8682	0.3644	100	0.3266	2041	2141	65
2.8682-2.9457	0.3367	110	0.3108	2633	2743	84
2.9457-3.0323	0.3555	147	0.3	2929	3076	93
3.0323-3.1301	0.3298	132	0.2942	3043	3175	98
3.1301-3.2419	0.3025	159	0.2842	3084	3243	99
3.2419-3.3717	0.3134	145	0.283	3188	3333	100
3.3717-3.525	0.3102	149	0.254	3139	3288	100
3.525-3.7107	0.2631	154	0.239	3178	3332	100
3.7107-3.9429	0.2908	148	0.2231	3123	3271	100
3.9429-4.2469	0.2404	156	0.2079	3160	3316	100
4.2469-4.6735	0.241	154	0.1794	3157	3311	100
4.6735-5.3479	0.2258	148	0.1813	3181	3329	100
5.3479-6.7307	0.2641	151	0.2309	3194	3345	100
6.7307-36.2432	0.2001	151	0.1757	3240	3391	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	3.226	-0.1198	0.4009	1.7813	-0.2347	2.3525	-0.071	-0.287	0.0024	0.1882	-0.0125	-0.0745	0.0976	-0.4026	0.0855	0.0627	-0.0034	0.0278	0.2735	-0.0163	0.2791	-36.504	56.7465	23.4467
2	3.0535	0.103	-1.213	0.814	0.0063	1.5607	-0.0121	0.4797	-0.172	-0.1596	-0.0361	0.3173	0.1375	-0.3457	0.0696	0.102	-0.0102	0.0168	0.2239	0.012	0.4018	-22.149	59.8302	3.5572
3	1.0167	0.3432	-0.215	2.6005	-0.4055	2.2735	0.0171	0.0722	-0.0632	-0.1571	0.0031	-0.0044	0.0735	0.0785	-0.0254	0.0886	0.0237	0.0137	0.0693	0.0729	0.1623	-1.2923	67.8988	0.1415
4	3.0251	-0.4367	0.886	3.0798	-0.6839	2.5715	-0.032	-0.3654	0.2664	0.9716	-0.2019	-0.2875	-0.7254	0.1863	-0.0199	0.0183	0.0287	0.1147	0.1839	0.0524	0.243	2.0107	75.9757	15.8901
5	0.2735	0.1927	-1.4266	0.7606	-2.7169	4.3533	-0.0666	0.3315	0.0907	-0.4702	0.252	0.363	0.2644	-0.3617	-0.0665	0.5691	-0.1134	-0.101	0.4011	0.0488	0.2699	3.8214	92.5805	-42.2352
6	3.8288	-1.3784	-1.3309	1.9688	0.5908	1.8335	0.192	0.3207	0.2861	-0.1682	-0.0192	-0.0868	-0.2835	0.0903	-0.1806	0.5771	-0.146	-0.051	0.4251	0.2002	0.4578	25.1838	103.533	-80.2288
7	1.8542	1.2363	-0.899	3.3364	-0.4898	1.6545	-0.0936	0.2912	-0.0697	-0.3917	0.1281	0.0983	0.2801	-0.1497	-0.0385	0.5647	-0.0828	-0.0751	0.3716	0.0628	0.3705	20.77	81.0053	-77.2541
8	1.6786	0.2961	0.6297	4.2557	-0.8345	2.014	0.3996	-0.0442	-0.3725	0.3306	-0.1758	-0.0571	-0.0355	-0.0922	-0.1856	0.6145	-0.0268	-0.1228	0.4132	0.073	0.5388	19.1645	51.1642	-58.6146
9	3.8152	-0.541	-1.464	4.3407	-3.2531	3.3829	0.4177	0.1399	0.6294	-0.0142	-0.1535	-0.8634	-0.2156	0.6692	-0.2412	0.8526	0.1375	-0.1383	0.6527	0.1179	1.2744	38.1899	33.5853	-57.7608
10	2.0786	-0.8781	-0.583	3.3684	-0.2142	2.5707	-0.1547	-0.5903	-0.2191	0.9564	-0.2175	-0.5441	0.0158	0.6674	0.2415	0.8343	-0.0913	-0.2453	0.5996	0.2048	0.7598	24.4809	42.9638	-46.8667

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 388 through 602 )	A	388 - 602
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 603 through 698 )	A	603 - 698
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 699 through 878 )	A	699 - 878
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 879 through 971)	A	879 - 971
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 972 through 1295)	A	972 - 1295
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 1296 through 1378)	A	1296 - 1378
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 1379 through 1579)	A	1379 - 1579
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 1580 through 1698)	A	1580 - 1698
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 1699 through 1751)	A	1699 - 1751
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 1752 through 1840)	A	1752 - 1840

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