PDB-4o87: Crystal structure of a N-tagged Nuclease

ID or keywords:

Entry

Database: PDB / ID: 4o87

Title

Crystal structure of a N-tagged Nuclease

Components

N-tagged Nuclease

Keywords

HYDROLASE / Novel fold / Nuclease

Function / homology

CITRIC ACID / Uncharacterized protein

Function and homology information

Biological species

Millerozyma acaciae (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Chakravarty, A.K. / Smith, P. / Shuman, S.

Citation

Journal: Cell Rep / Year: 2014
Title: Structure, mechanism, and specificity of a eukaryal tRNA restriction enzyme involved in self-nonself discrimination.
Authors: Chakravarty, A.K. / Smith, P. / Jalan, R. / Shuman, S.

History

Deposition	Dec 26, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 15, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.2	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	4o87.cif.gz	294.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4o87.ent.gz	241.2 KB	Display	PDB format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o8/4o87 ftp://data.pdbj.org/pub/pdb/validation_reports/o8/4o87	HTTPS FTP

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Related structure data

Related structure data	4o88C C: citing same article (ref.)
Similar structure data	4o88-d 6guu-d 6mnz-d 5hp6-d 3ou7-d 5z5h-1 4z64-d 5hek-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: N-tagged Nuclease

B: N-tagged Nuclease

hetero molecules

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

1

Idetical with deposited unit
defined by author

2

Idetical with deposited unit
defined by author

3

A: N-tagged Nuclease

B: N-tagged Nuclease

hetero molecules

A: N-tagged Nuclease

B: N-tagged Nuclease

hetero molecules

defined by author&software
151 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.870, 77.430, 147.750
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	N-tagged Nuclease Mass: 36309.824 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Millerozyma acaciae (fungus) / Plasmid: pET28b-Smt3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q707V3
#2: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 724 / 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: 2.44 Å³/Da / Density % sol: 49.52 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 100 mM Sodium citrate, 3 - 3.5 M Ammonium sulfate, 100 mM Magnesium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 130 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2012
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.8→38.53 Å / Num. all: 66634 / Num. obs: 66634 / % possible obs: 100 % / Observed criterion σ(F): 9999 / Observed criterion σ(I): 9999
Reflection shell	Resolution: 1.8→1.84 Å / % possible all: 100

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Processing

Software

Name	Version	Classification
CBASS		data collection
PHENIX		model building
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
MOSFLM		data reduction
Aimless		data scaling
SCALA		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→38.532 Å / SU ML: 0.19 / σ(F): 1.33 / Phase error: 20.8 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1991	2517	3.79 %
R_work	0.1591	-	-
obs	0.1606	66334	99.66 %
all	-	66634	-

Solvent computation

Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.8→38.532 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5076	0	161	724	5961

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	5521
X-RAY DIFFRACTION	f_angle_d	1.297	7512
X-RAY DIFFRACTION	f_dihedral_angle_d	14.866	2131
X-RAY DIFFRACTION	f_chiral_restr	0.067	826
X-RAY DIFFRACTION	f_plane_restr	0.006	961

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 (%)
1.8-1.8346	0.3519	121	0.2512	3478	X-RAY DIFFRACTION	99
1.8346-1.8721	0.2614	132	0.23	3494	X-RAY DIFFRACTION	99
1.8721-1.9128	0.2423	141	0.1952	3456	X-RAY DIFFRACTION	99
1.9128-1.9573	0.2437	158	0.1874	3462	X-RAY DIFFRACTION	99
1.9573-2.0062	0.2113	140	0.1716	3500	X-RAY DIFFRACTION	99
2.0062-2.0605	0.2193	139	0.1597	3529	X-RAY DIFFRACTION	100
2.0605-2.1211	0.1947	140	0.1572	3507	X-RAY DIFFRACTION	100
2.1211-2.1896	0.1812	137	0.1552	3500	X-RAY DIFFRACTION	100
2.1896-2.2678	0.2145	138	0.1541	3522	X-RAY DIFFRACTION	100
2.2678-2.3586	0.2267	140	0.1575	3545	X-RAY DIFFRACTION	100
2.3586-2.4659	0.2035	138	0.161	3534	X-RAY DIFFRACTION	100
2.4659-2.5959	0.21	139	0.1661	3542	X-RAY DIFFRACTION	100
2.5959-2.7585	0.2019	139	0.1725	3546	X-RAY DIFFRACTION	100
2.7585-2.9714	0.2211	141	0.164	3581	X-RAY DIFFRACTION	100
2.9714-3.2703	0.1985	140	0.164	3580	X-RAY DIFFRACTION	100
3.2703-3.7432	0.1725	142	0.1366	3582	X-RAY DIFFRACTION	100
3.7432-4.7147	0.1511	145	0.121	3669	X-RAY DIFFRACTION	100
4.7147-38.5412	0.1942	147	0.1699	3789	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	2.8054	0.3936	-0.0745	0.4198	0.1334	1.1578	-0.0494	0.1774	-0.05	0.0703	0.0693	-0.0064	0.0696	0.0812	-0.0028	0.1079	0.0174	0.0008	0.0396	-0.0175	0.1039	6.3927	38.9784	68.7048
2	1.2187	-0.0033	0.0101	0.4861	-0.1192	0.0095	-0.1689	-0.0042	-0.2074	0.0844	0.1074	-0.0975	0.2535	-0.0131	-0.0059	0.151	-0.0177	0.0312	0.0696	-0.0133	0.1283	-21.983	29.9523	83.0892
3	1.7133	0.3987	-0.5881	0.649	0.4937	1.1245	0.0155	-0.1181	-0.0266	0.0921	0.0137	-0.0497	0.0921	0.0872	0.0972	0.131	0.0259	-0.0141	0.0149	0.0146	0.1128	4.3459	41.3914	75.9157
4	2.4272	0.8544	-0.1332	1.6725	-0.2189	1.3949	0.0417	-0.1316	-0.1331	0.1277	0.0054	0.0241	-0.008	-0.0062	0.0054	0.1369	0.0143	0.0147	0.0815	-0.0007	0.1263	-24.3933	35.2858	88.55
5	2.316	0.5248	-1.0059	0.7408	0.1587	0.93	-0.0397	-0.3713	-0.0885	0.2249	0.0096	-0.168	0.0009	0.235	0.064	0.2192	0.0091	0.0005	0.113	-0.002	0.201	-6.0389	46.4006	87.0816
6	2.2165	0.0332	-1.157	0.5069	0.1156	1.4904	-0.1503	-0.3112	-0.0327	0.3796	0.1713	-0.351	0.1637	0.8223	-0.036	0.3489	0.0511	-0.0624	0.4853	-0.1195	0.3966	20.816	47.8078	81.281
7	2.3437	-0.2829	-0.4292	0.3431	-0.2186	1.1231	0.0322	0.3057	-0.1022	-0.0942	0.0043	0.0546	0.0346	-0.0781	-0.0047	0.1294	0.0007	-0.0059	0.1792	0.0086	0.1406	-6.3549	36.5797	128.4165
8	1.6668	-0.1912	-1.8848	0.0974	-0.088	0.8892	-0.0932	0.5071	-0.1942	-0.1327	-0.0458	0.0595	0.0418	-0.1203	0.0099	0.2195	0.0136	-0.0152	0.3521	-0.0523	0.1839	4.3139	32.0092	117.564
9	0.6112	-0.005	-0.4079	0.784	0.0401	0.4329	0.3774	0.2639	0.5037	-0.2863	-0.1036	-0.061	-0.4357	0.0052	0.0298	0.2676	0.0322	0.064	0.3028	0.11	0.2187	7.8536	46.3583	115.2895
10	1.9885	-0.4761	-0.9575	1.4844	-0.0919	2.9059	0.0063	-0.2609	-0.1723	-0.019	0.0732	-0.1	0.3044	0.3023	0	0.2506	0.0047	0.0007	0.3452	0.0049	0.1688	26.8113	31.0578	109.3707
11	2.0433	-1.0537	-0.8221	1.0925	0.0476	0.5842	0.3999	0.7489	-0.2057	-0.5064	-0.068	0.1627	-0.3989	-0.5634	0.0699	0.3461	0.039	0.0437	0.4122	0.0577	0.3093	6.3984	45.039	110.2903
12	0.3399	1.1493	0.113	4.389	1.3347	1.6745	0.0532	0.6802	0.6604	-0.6631	-0.2331	0.752	0.0412	-0.8916	-1.2753	0.3609	0.049	-0.0599	0.8877	0.254	0.4669	-22.4698	45.2687	116.7988

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 84 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 85 through 111 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 112 through 178 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 179 through 261 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 262 through 296 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 297 through 319 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 0 through 84 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 85 through 154 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 155 through 198 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 199 through 261 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 262 through 296 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 297 through 318 )

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