PDB-4nck: Crystal Structure of Pyrococcus furiosis Rad50 R797G mutation

ID or keywords:

Entry

Database: PDB / ID: 4nck

Title

Crystal Structure of Pyrococcus furiosis Rad50 R797G mutation

Components

DNA double-strand break repair Rad50 ATPase

Keywords

DNA BINDING PROTEIN / Adenosine Triphosphatase / DNA Repair / Fungal Protein

Function / homology

Function and homology information

double-strand break repair / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding
Similarity search - Function

Biological species

Pyrococcus furiosus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.99 Å

Authors

Classen, S. / Williams, G.J. / Arvai, A.S. / Williams, R.S.

Citation

Journal: Embo J. / Year: 2014
Title: ATP-driven Rad50 conformations regulate DNA tethering, end resection, and ATM checkpoint signaling.
Authors: Deshpande, R.A. / Williams, G.J. / Limbo, O. / Williams, R.S. / Kuhnlein, J. / Lee, J.H. / Classen, S. / Guenther, G. / Russell, P. / Tainer, J.A. / Paull, T.T.

History

Deposition	Oct 24, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 5, 2014	Provider: repository / Type: Initial release
Revision 1.1	Apr 2, 2014	Group: Database references
Revision 1.2	Aug 2, 2017	Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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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PDBx/mmCIF format	4nck.cif.gz	358.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4nck_validation.pdf.gz	460.2 KB	Display	wwPDB validaton report
Full document	4nck_full_validation.pdf.gz	466.9 KB	Display
Data in XML	4nck_validation.xml.gz	26.7 KB	Display
Data in CIF	4nck_validation.cif.gz	38.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nc/4nck ftp://data.pdbj.org/pub/pdb/validation_reports/nc/4nck	HTTPS FTP

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Related structure data

Related structure data	4nchC 4nciC 4ncjC C: citing same article (ref.)
Similar structure data	5t8p-1 5t8q-2 5ef4-2 4g3e-2 6zgy-1 1k47-6 2qoc-d 6vzh-3 5zv2-2 3zos-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: DNA double-strand break repair Rad50 ATPase

B: DNA double-strand break repair Rad50 ATPase

hetero molecules

77.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DNA double-strand break repair Rad50 ATPase

defined by author&software
38.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: DNA double-strand break repair Rad50 ATPase

hetero molecules

defined by author&software
38.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	49.669, 68.065, 202.900
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

#1: Protein	DNA double-strand break repair Rad50 ATPase Mass: 38508.473 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-177 AND 726-882 / Mutation: R797G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1167, rad50 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: P58301
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.23 Å³/Da / Density % sol: 44.76 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.6 Details: 100 mM Bicine, 6-14% PEG 20000, 2 mM Dioxane, pH 8.6, vapor diffusion, sitting drop, temperature 293K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	90	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SSRL	BL11-1	1	0.97945
SYNCHROTRON	ALS	12.3.1	2	1.11583

Detector

Type	ID	Detector
MARMOSAIC 325 mm CCD	1	CCD
MARMOSAIC 325 mm CCD	2	CCD

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Si 111 DOUBLE CRYSTAL	SINGLE WAVELENGTH	M	x-ray	1
2	Si 111 DOUBLE CRYSTAL	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97945	1
2	1.11583	1

Reflection

Resolution: 1.99→50 Å / Num. obs: 89299 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 42.92 Å² / R_merge(I) obs: 0.036 / Net I/σ(I): 16.22

Reflection shell

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.99-2.05		0.784	1.4	1,2	95.5
2.05-2.11		0.655	1.81	1,2	99.8
2.11-2.17		0.479	2.5	1,2	99.9
2.17-2.23		0.329	3.64	1,2	99.8
2.23-2.31		0.266	4.42	1,2	99.9
2.31-2.39		0.213	5.56	1,2	99.9
2.39-2.48		0.156	7.26	1,2	99.9
2.48-2.58		0.116	9.7	1,2	99.9
2.58-2.69		0.092	12.06	1,2	99.7
2.69-2.82		0.071	15.79	1,2	99.7
2.82-2.98		0.056	19.72	1,2	99.4
2.98-3.16		0.042	24.93	1,2	98.8
3.16-3.38		0.033	30.2	1,2	98.6
3.38-3.65		0.027	37.07	1,2	98.4
3.65-3.99		0.024	40.17	1,2	97.2
3.99-4.47		0.022	44.59	1,2	97
4.47-5.16		0.021	45.75	1,2	97.2
5.16-6.32		0.021	44.34	1,2	97.4
6.32-8.93		0.019	46.87	1,2	97.7
	8.93	0.017	47.41	1,2	87.5

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
MOLREP		phasing
PHENIX	dev_1233	refinement
PDB_EXTRACT	3.11	data extraction
Blu-Ice		data collection
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.99→48.245 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.23 / σ(F): 1.21 / Phase error: 23.22 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2298	3760	4.21 %
R_work	0.181	-	-
obs	0.1831	89253	98.58 %

Solvent computation

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

Displacement parameters

B_iso mean: 62.3288 Å²

Refinement step

Cycle: LAST / Resolution: 1.99→48.245 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4629	0	7	324	4960

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	4738
X-RAY DIFFRACTION	f_angle_d	1.274	6430
X-RAY DIFFRACTION	f_dihedral_angle_d	12.645	1695
X-RAY DIFFRACTION	f_chiral_restr	0.071	776
X-RAY DIFFRACTION	f_plane_restr	0.006	811

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 (%)
1.99-2.0198	0.2968	120	0.3028	2717	X-RAY DIFFRACTION	85
2.0198-2.0464	0.3154	139	0.2826	3242	X-RAY DIFFRACTION	100
2.0464-2.0744	0.3357	141	0.2833	3244	X-RAY DIFFRACTION	100
2.0744-2.1041	0.311	139	0.2571	3194	X-RAY DIFFRACTION	100
2.1041-2.1355	0.2451	140	0.2439	3185	X-RAY DIFFRACTION	100
2.1355-2.1688	0.2931	142	0.2299	3213	X-RAY DIFFRACTION	100
2.1688-2.2044	0.2721	132	0.2161	3187	X-RAY DIFFRACTION	100
2.2044-2.2424	0.2301	144	0.2019	3231	X-RAY DIFFRACTION	100
2.2424-2.2832	0.2848	142	0.2091	3213	X-RAY DIFFRACTION	100
2.2832-2.3271	0.2331	141	0.2101	3175	X-RAY DIFFRACTION	100
2.3271-2.3746	0.2398	145	0.2066	3260	X-RAY DIFFRACTION	100
2.3746-2.4262	0.2316	139	0.1892	3171	X-RAY DIFFRACTION	100
2.4262-2.4827	0.2113	146	0.1816	3233	X-RAY DIFFRACTION	100
2.4827-2.5447	0.2107	142	0.1705	3176	X-RAY DIFFRACTION	100
2.5447-2.6135	0.2243	145	0.1777	3247	X-RAY DIFFRACTION	100
2.6135-2.6904	0.2367	139	0.1773	3149	X-RAY DIFFRACTION	100
2.6904-2.7773	0.2711	139	0.1764	3244	X-RAY DIFFRACTION	100
2.7773-2.8765	0.2702	130	0.1772	3178	X-RAY DIFFRACTION	100
2.8765-2.9917	0.2729	140	0.1884	3151	X-RAY DIFFRACTION	99
2.9917-3.1278	0.2767	140	0.1893	3206	X-RAY DIFFRACTION	99
3.1278-3.2927	0.2552	145	0.1904	3154	X-RAY DIFFRACTION	99
3.2927-3.4989	0.2144	134	0.1697	3191	X-RAY DIFFRACTION	98
3.4989-3.769	0.232	142	0.162	3143	X-RAY DIFFRACTION	98
3.769-4.1481	0.2413	140	0.1565	3114	X-RAY DIFFRACTION	97
4.1481-4.7479	0.1802	135	0.1369	3090	X-RAY DIFFRACTION	97
4.7479-5.9801	0.1952	140	0.1751	3148	X-RAY DIFFRACTION	97
5.9801-48.2586	0.214	139	0.2007	3037	X-RAY DIFFRACTION	95

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	5.0988	1.102	0.6394	4.5646	-0.3539	4.1516	0.1317	-0.2728	0.4405	0.1377	-0.0294	0.0297	-0.5899	-0.083	-0.0987	0.2275	0.0076	-0.0121	0.1817	-0.0674	0.2403	23.623	4.9821	43.6789
2	2.2565	1.2757	0.9642	4.7541	0.5612	4.8822	0.0964	-0.2164	0.2999	0.4151	-0.0571	0.5489	-0.3376	-0.4899	-0.0057	0.2324	0.0469	0.0823	0.2297	-0.0314	0.363	16.8086	-1.1567	47.807
3	4.4392	0.9257	1.844	4.3054	-0.0947	4.5929	-0.0252	-0.8301	-0.3306	2.4308	-0.1724	-0.5809	-0.896	0.4989	-0.0707	1.3968	-0.1233	-0.3963	0.5473	-0.0002	0.2862	33.5029	-3.9372	70.5804
4	3.3289	-0.1164	1.5113	3.0206	-0.4451	3.4053	0.0113	-0.1217	0.2024	0.6225	0.013	-0.7848	-0.6085	0.6525	0.0207	0.3469	-0.0701	-0.0372	0.354	-0.1291	0.3807	36.998	5.1623	47.8661
5	5.0673	-0.0342	0.1411	2.8997	1.1351	2.2589	0.0616	0.6969	0.2362	-0.7009	0.4263	-0.5887	-0.6328	0.8347	-0.4047	0.425	-0.1451	0.1358	0.523	-0.1196	0.3593	-12.6933	-2.4842	20.8569
6	3.6151	-0.5341	0.673	2.894	1.448	3.7301	0.0316	0.1866	0.1087	-0.395	0.5104	-0.6922	-0.0581	1.3677	-0.4445	0.3566	-0.022	0.0736	0.6616	-0.2184	0.5425	-7.2463	-10.7127	19.9022
7	2.8717	-1.6833	-0.9437	5.5125	0.7429	4.7727	0.0974	1.0254	-0.7282	-1.0637	-0.1596	0.4772	0.174	-0.5036	0.0167	0.7008	-0.0649	-0.1064	0.6582	-0.2482	0.4982	-24.6642	-22.9345	1.0573
8	4.6755	0.0652	-0.287	4.7523	1.1288	4.838	0.0525	0.7097	0.2833	-1.1229	0.0528	0.4496	-0.7123	-0.3374	-0.0887	0.4844	0.0175	-0.0438	0.3929	0.0028	0.2713	-26.6441	-3.5696	16.412

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 1:55)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 56:162)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 732:815)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 816:882)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 1:55)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 56:162)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 730:815)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 816:882)

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