PDB-5da9: ATP-gamma-S bound Rad50 from Chaetomium thermophilum in complex w...

ID or keywords:

Entry

Database: PDB / ID: 5da9

Title

ATP-gamma-S bound Rad50 from Chaetomium thermophilum in complex with the Rad50-binding domain of Mre11

Components

Putative double-strand break protein
Putative uncharacterized protein,Putative uncharacterized protein

Keywords

HYDROLASE /

ATPase / ATPyS bound

Function / homology

Function and homology information

Mre11 complex / 3'-5'-DNA exonuclease activity /

telomere maintenance / guanyl-nucleotide exchange factor activity / DNA endonuclease activity / meiotic cell cycle / double-strand break repair / manganese ion binding /

ATP hydrolysis activity /

metal ion binding
Similarity search - Function

Biological species

Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3 Å

Authors

Seifert, F.U. / Lammens, K. / Stoehr, G. / Kessler, B. / Hopfner, K.-P.

Citation

Journal: Embo J. / Year: 2016
Title: Structural mechanism of ATP-dependent DNA binding and DNA end bridging by eukaryotic Rad50.
Authors: Seifert, F.U. / Lammens, K. / Stoehr, G. / Kessler, B. / Hopfner, K.P.

History

Deposition	Aug 19, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Mar 2, 2016	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5da9.cif.gz	413.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5da9.ent.gz	351.2 KB	Display	PDB format
PDBx/mmJSON format	5da9.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/da/5da9 ftp://data.pdbj.org/pub/pdb/validation_reports/da/5da9	HTTPS FTP

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Related structure data

Related structure data	5dacC C: citing same article (ref.)
Similar structure data	6pb0-d 6yt0-1 8623 1y5l-d 0257 1siw-d 6boy-d 2q06-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	#225 - Sep 2018 Phytase similarity (3) #148 - Apr 2012 Ras Protein similarity (2) #150 - Jun 2012 Sliding Clamps similarity (1)

Deposited unit

A: Putative uncharacterized protein,Putative uncharacterized protein

B: Putative uncharacterized protein,Putative uncharacterized protein

C: Putative double-strand break protein

D: Putative double-strand break protein

hetero molecules

128 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	116.511, 125.086, 168.304
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

#1: Protein	Putative uncharacterized protein,Putative uncharacterized protein Mass: 50827.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Gene: CTHT_0073630 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SHW7
#2: Protein	Putative double-strand break protein Mass: 12716.786 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Gene: CTHT_0007600 / Production host: Escherichia coli (E. coli) / References: UniProt: G0RYR3
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₂P₃S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 49.02 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M sodium chloride, 0.1 M magnesium chloride, 11% PEG 1500, 0.1 M Hepes buffer

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9797 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9797 Å / Relative weight: 1
Reflection	Resolution: 3→50 Å / Num. obs: 47393 / % possible obs: 99.2 % / Redundancy: 6.9 % / R_sym value: 0.074 / Net I/σ(I): 14.83
Reflection shell	Resolution: 3→3.18 Å / Redundancy: 6.7 % / R_merge(I) obs: 1.114 / Mean I/σ(I) obs: 1.58 / % possible all: 95.5

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XDS		data scaling
SHARP		phasing
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 3→47.898 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2576	2363	4.99 %
R_work	0.2161	-	-
obs	0.2182	47386	99.23 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3→47.898 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7736	0	64	14	7814

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	7905
X-RAY DIFFRACTION	f_angle_d	1.04	10655
X-RAY DIFFRACTION	f_dihedral_angle_d	12.664	3019
X-RAY DIFFRACTION	f_chiral_restr	0.046	1228
X-RAY DIFFRACTION	f_plane_restr	0.004	1366

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 (%)
2.9956-3.0567	0.4636	130	0.4687	2292	X-RAY DIFFRACTION	88
3.0567-3.1232	0.4616	127	0.3771	2655	X-RAY DIFFRACTION	100
3.1232-3.1958	0.4081	143	0.3172	2705	X-RAY DIFFRACTION	100
3.1958-3.2757	0.3256	138	0.2854	2631	X-RAY DIFFRACTION	100
3.2757-3.3642	0.296	141	0.27	2694	X-RAY DIFFRACTION	100
3.3642-3.4632	0.3548	141	0.2617	2669	X-RAY DIFFRACTION	100
3.4632-3.575	0.3216	140	0.2582	2667	X-RAY DIFFRACTION	100
3.575-3.7027	0.3145	139	0.2302	2650	X-RAY DIFFRACTION	100
3.7027-3.8509	0.2748	141	0.2173	2689	X-RAY DIFFRACTION	100
3.8509-4.0261	0.245	140	0.2215	2688	X-RAY DIFFRACTION	100
4.0261-4.2382	0.3169	137	0.2118	2654	X-RAY DIFFRACTION	100
4.2382-4.5035	0.2809	139	0.1868	2676	X-RAY DIFFRACTION	100
4.5035-4.851	0.1653	145	0.1673	2678	X-RAY DIFFRACTION	100
4.851-5.3386	0.2707	138	0.1844	2658	X-RAY DIFFRACTION	100
5.3386-6.1097	0.25	141	0.2231	2665	X-RAY DIFFRACTION	100
6.1097-7.6924	0.2631	140	0.2304	2673	X-RAY DIFFRACTION	100
7.6924-47.9043	0.2014	143	0.1933	2679	X-RAY DIFFRACTION	100

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	2.8794	-0.1605	-1.7083	0.359	-0.2529	1.8479	0.0016	-0.2541	-0.5863	-0.0969	-0.0948	-0.1355	0.1894	0.8217	0.0029	0.6121	-0.1121	0.0224	0.7811	0.015	0.6939	-4.9709	-31.9816	-47.3711
2	0.5471	0.2191	-1.0706	1.7824	1.2329	3.1496	0.5732	-0.2154	-0.18	-0.8914	0.2791	-0.098	-1.1327	-1.1267	0.9197	1.2624	0.1561	0.204	0.5215	-0.0106	0.667	-21.9846	-14.4947	-73.6009
3	1.9987	-0.068	-0.3155	1.9334	0.5842	2.7178	0.0771	0.0576	-0.5108	0.07	-0.1899	0.1811	0.3649	-0.2482	0.0006	0.5933	-0.2006	0.0072	0.5975	0.0795	0.7099	-25.5311	-37.2568	-43.0775
4	1.5261	-0.7398	1.1891	0.9754	-1.0706	1.42	0.2914	0.4079	0.4639	-0.1211	-0.2067	0.0975	-0.6727	-0.7016	-0.0451	0.9878	0.2891	0.3534	0.7612	0.3838	0.8662	-42.1269	-2.3945	-30.1092
5	-0.7742	-0.3748	-1.9732	2.7457	2.6447	-0.3493	0.4761	0.0132	-0.0072	0.0616	0.104	-0.6988	0.0861	0.5949	0.5305	0.8814	-0.4505	-0.0021	0.866	0.0592	0.9236	-12.7075	-2.7489	-21.9558
6	1.2715	0.1393	-0.7676	0.9496	-0.2808	0.5103	0.5195	-0.1075	-0.2707	-0.0884	-0.226	0.551	-0.2103	-0.6847	0.0191	0.707	-0.235	0.1415	0.7107	0.0578	0.768	-32.0167	-21.9146	-18.5859
7	0.0908	0.1939	0.1928	0.7519	0.8041	0.8419	0.3188	0.9319	-0.1651	0.0101	0.2999	1.3577	0.9947	-0.704	-0.0707	0.6428	0.0066	-0.0519	1.1963	0.1532	0.8401	-49.7608	-21.0638	-27.7444
8	0.6867	-0.4027	-0.4031	0.2484	0.2229	0.2147	-0.426	0.9705	1.4264	-1.6905	0.9855	-0.55	-0.7059	-0.4429	-0.0027	1.4477	-0.4449	-0.1111	1.1977	-0.2054	1.0515	-24.5312	-25.5171	-79.1862
9	3.2564	0.1232	0.7724	0.0279	0.0038	0.7691	-0.2275	0.4179	0.6964	0.7647	-0.104	-1.6937	-0.255	0.1863	0.0532	1.4603	-0.068	-0.0046	0.5348	-0.1867	1.0461	-15.027	-22.3294	-82.4854
10	0.0673	0.0447	0.0687	0.074	0.0361	0.0522	0.9627	0.1404	-0.1443	-0.1078	0.8062	-0.3416	-0.0537	0.5454	0.0017	1.7163	0.2259	0.3405	1.4247	-0.2037	1.3025	-5.4943	-18.5616	-72.608
11	2.956	-1.4686	0.8504	1.1098	-0.0572	0.6669	0.0212	1.1081	-0.223	-0.8742	0.2063	-0.8138	-0.6998	0.9457	-0.0052	0.7274	-0.3068	0.2142	0.7311	-0.4562	1.6527	-5.0109	-19.595	-91.3752
12	0.4922	0.202	-0.1504	0.1461	-0.1026	0.0677	-0.986	0.3371	-0.6191	-1.0627	-1.0203	-0.0971	-0.1023	0.2572	-0.0215	1.6847	-0.4965	0.0299	3.0119	-0.4487	1.3565	-10.5267	-20.5029	-111.06
13	0.6015	0.0072	-0.3166	0.0331	-0.0484	0.1719	-0.7108	0.1287	-1.5694	0.5418	-0.0916	0.1463	0.4505	-0.3824	-0.6099	2.1739	-0.4789	-0.0078	1.1952	0.0554	1.4716	-13.4625	-27.5636	-94.8256
14	2.7591	0.7002	2.6943	4.6049	2.8032	3.6785	1.0752	0.4915	0.1626	1.7726	0.5745	1.0483	-0.0598	-1.8376	1.9349	0.972	-0.2199	0.3966	1.6733	0.1915	1.0013	-15.6124	13.6714	-8.1814
15	0.3616	0.3403	-0.125	0.1572	0.5647	0.1405	0.1395	-0.3449	0.6446	0.0645	0.3849	0.5559	0.2212	-0.0546	0.117	0.4899	0.0412	0.261	1.1013	-0.3606	1.5572	-19.7811	21.8506	-8.987

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 153 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 154 through 1208 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1209 through 1311 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 153 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 154 through 1227 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1228 through 1290 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1291 through 1312 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 438 through 451 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 452 through 471 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 472 through 476 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 477 through 495 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 496 through 504 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 505 through 531 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 439 through 471 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 472 through 524 )

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