PDB-3nkd: Structure of CRISP-associated protein Cas1 from Escherichia coli ...

ID or keywords:

Entry

Database: PDB / ID: 3nkd

Title

Structure of CRISP-associated protein Cas1 from Escherichia coli str. K-12

Components

CRISPR-associated protein Cas1

Keywords

IMMUNE SYSTEM / CRISPR / Cas1 / YgbT / Nuclease / DNA recombination / DNA repair

Function / homology

Function and homology information

CRISPR-cas system / crossover junction DNA endonuclease activity / 5'-flap endonuclease activity / maintenance of CRISPR repeat elements / defense response to virus / Hydrolases; Acting on ester bonds / DNA repair / DNA damage response / protein homodimerization activity / DNA binding ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Nocek, B. / Skarina, T. / Beloglazova, N. / Savchenko, A. / Joachimiak, A. / Yakunin, A.

Citation

Journal: Mol.Microbiol. / Year: 2011
Title: A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair.
Authors: Babu, M. / Beloglazova, N. / Flick, R. / Graham, C. / Skarina, T. / Nocek, B. / Gagarinova, A. / Pogoutse, O. / Brown, G. / Binkowski, A. / Phanse, S. / Joachimiak, A. / Koonin, E.V. / ...

History

Deposition	Jun 18, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 25, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3nkd.cif.gz	214.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3nkd.ent.gz	183.6 KB	Display	PDB format
PDBx/mmJSON format	3nkd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3nkd_validation.pdf.gz	429.2 KB	Display	wwPDB validaton report
Full document	3nkd_full_validation.pdf.gz	433.9 KB	Display
Data in XML	3nkd_validation.xml.gz	22.7 KB	Display
Data in CIF	3nkd_validation.cif.gz	33 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nk/3nkd ftp://data.pdbj.org/pub/pdb/validation_reports/nk/3nkd	HTTPS FTP

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Related structure data

Related structure data	3nkeC 3god C: citing same article (ref.)
Similar structure data	6sy6-d 5zzb-1 2btf-d 3chw-d 6ke1-d 1k7y-d 6sy4-d 3iva-d 3hv1-d 1l8w-5 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	#181 - Jan 2015 Cascade and CRISPR similarity (9)

Deposited unit

A: CRISPR-associated protein Cas1

B: CRISPR-associated protein Cas1

66.5 kDa, 2 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)	78.674, 79.300, 101.562
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	CRISPR-associated protein Cas1 Mass: 33235.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: EcDH1_0933 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: C9R0C6, UniProt: Q46896*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.38 Å³/Da / Density % sol: 48.39 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M bis-Tris, 0.1 M Na formate, 0.1 M Li-sulfate, 0.3M NDSB 211, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2010 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.95→35.24 Å / Num. all: 47050 / Num. obs: 46873 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.6 % / B_iso Wilson estimate: 35.4 Å² / R_merge(I) obs: 0.095 / Net I/σ(I): 25
Reflection shell	Resolution: 1.95→1.98 Å / Redundancy: 9.6 % / R_merge(I) obs: 0.55 / Mean I/σ(I) obs: 4 / Num. unique all: 2330 / % possible all: 100

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→35.24 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.915 / SU B: 10.028 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25855	2336	5.1 %	RANDOM
R_work	0.21723	-	-	-
all	0.22	46061	-	-
obs	0.21959	43725	98.43 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 26.92 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.32 Å²	0 Å²	0 Å²
2-	-	0.1 Å²	0 Å²
3-	-	-	0.22 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→35.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3976	0	0	266	4242

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.022	4046
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2803
X-RAY DIFFRACTION	r_angle_refined_deg	1.71	1.977	5484
X-RAY DIFFRACTION	r_angle_other_deg	0.986	3	6790
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.825	5	518
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.611	22.037	162
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.421	15	675
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.616	15	43
X-RAY DIFFRACTION	r_chiral_restr	0.112	0.2	638
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	4494
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	845
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.992	1.5	2592
X-RAY DIFFRACTION	r_mcbond_other	0.287	1.5	1062
X-RAY DIFFRACTION	r_mcangle_it	1.738	2	4156
X-RAY DIFFRACTION	r_scbond_it	2.695	3	1454
X-RAY DIFFRACTION	r_scangle_it	4.437	4.5	1328
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.95→2.004 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.352	182	-
R_work	0.3	3193	-
obs	-	-	98.86 %

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	4.3366	-2.0055	-3.4288	4.7413	3.082	3.2987	0.0138	0.0105	0.0155	0.0399	0.0378	-0.0878	0.008	0.0178	-0.0515	0.0176	0.0285	-0.0319	0.1478	0.0043	0.0897	33.4329	33.9607	25.9732
2	3.5638	1.3395	-2.7177	3.4999	-0.1143	2.6615	-0.0165	-0.1468	0.1298	0.3537	0.0496	-0.0195	0.0501	0.0654	-0.0331	0.0651	0.0019	-0.023	0.1833	-0.0108	0.1091	34.1867	45.042	33.5877
3	1.1271	0.5034	-0.378	1.8834	-0.0214	0.5744	0.0202	-0.1605	-0.0443	0.1762	0.0061	0.0571	-0.0093	0.0331	-0.0264	0.0252	0.0054	-0.0116	0.1338	-0.0086	0.0733	32.5013	40.6864	29.5743
4	8.4685	-3.6043	-5.8835	6.901	4.0613	9.0732	0.1226	0.0107	0.3466	-0.2669	0.1473	-0.3462	-0.2994	0.086	-0.2699	0.0204	-0.0129	0.0055	0.1094	0.0171	0.1001	36.1628	48.3042	20.526
5	0.4087	0.1504	0.3257	2.415	0.1795	1.6822	-0.0125	0.0344	0.046	0.1188	0.0498	0.1356	0.028	-0.1491	-0.0374	0.0088	0.0074	-0.0021	0.1367	0.0021	0.1169	24.5275	35.799	19.7712
6	0.3444	-0.3674	-0.0502	3.0176	0.2155	0.956	0.0334	0.0927	0.0017	-0.1741	-0.0428	-0.1914	0.1751	0.0404	0.0095	0.0896	0.0085	-0.0108	0.0534	-0.0159	0.0576	32.9835	19.6786	1.128
7	3.4343	2.385	-0.6204	2.0967	-0.7359	0.3234	-0.1171	-0.018	-0.0015	-0.093	0.1914	0.075	0.0376	-0.1519	-0.0742	0.2524	0.0639	-0.0935	0.1397	0.0055	0.0782	24.2965	8.4026	4.9642
8	4.4436	-1.5051	1.7788	3.1218	-0.8757	3.8068	0.0979	-0.0418	-0.2063	-0.1258	0.0085	0.2296	0.3709	-0.0462	-0.1064	0.0472	-0.0154	-0.0377	0.0677	0.0144	0.1236	27.8566	2.4266	22.8427
9	5.6872	2.2732	1.9034	2.6595	5.1019	11.4156	0.3169	0.1861	0.0434	0.2141	-0.1435	-0.0205	0.2651	-0.4332	-0.1734	0.3106	0.0703	0.0687	0.2003	0.0736	0.355	17.4672	7.1292	27.9038
10	0.7755	1.145	-0.414	6.3412	-2.359	1.2583	-0.0276	-0.0653	-0.0864	0.1915	0.0304	0.2152	-0.1531	-0.0604	-0.0028	0.0358	0.0076	0.021	0.1141	0.0071	0.1158	23.1371	19.1317	22.7476
11	0.4699	-0.6544	0.2804	4.4944	-0.0815	1.9255	0.0744	0.0764	0.0443	-0.1334	-0.0187	0.2152	0.1614	0.0463	-0.0557	0.0216	0.0028	-0.009	0.1174	0.0033	0.098	25.423	25.0904	8.4183
12	5.0457	-1.1671	0.8199	4.4063	-5.5889	7.4925	-0.066	-0.0958	-0.0117	0.1283	0.0605	-0.0527	-0.1681	0.0496	0.0055	0.0738	0.0155	-0.0064	0.0599	0.0044	0.0966	30.0283	12.6597	23.6762
13	5.7557	-7.487	-4.307	9.7726	5.6265	3.2532	-0.3183	-0.4286	0.109	0.4837	0.4976	-0.1676	0.2952	0.3631	-0.1793	0.523	0.0178	-0.0393	0.3605	-0.0629	0.2063	28.323	10.1527	38.064
14	2.5434	1.2336	-2.8799	0.7869	-1.564	4.6883	0.0475	-0.0789	-0.0173	0.0999	-0.0251	0.0116	0.0233	0.1946	-0.0224	0.0873	0.0298	-0.0074	0.0469	-0.0037	0.0893	30.1804	21.8668	27.0415
15	0.391	1.1347	0.3114	8.0019	-4.6238	7.3101	-0.0062	-0.0005	-0.0742	0.0222	-0.0786	-0.3839	0.0537	0.3556	0.0848	0.037	0.0332	0.0353	0.1339	-0.034	0.1431	39.9863	25.3358	2.6334
16	7.8663	2.3926	5.3487	2.2489	3.4357	5.919	0.0697	0.0855	0.1812	-0.0966	-0.0903	0.0922	-0.1157	-0.1713	0.0206	0.0989	0.0243	-0.0008	0.156	0.0686	0.1854	12.7754	53.0791	11.8405
17	5.3234	2.4067	-0.3166	5.1534	0.9477	3.4901	-0.0387	0.0181	0.3443	-0.0625	0.096	-0.1073	-0.2861	-0.0998	-0.0573	0.07	0.0642	0.0097	0.1178	0.039	0.1139	15.7015	50.7017	28.1079
18	2.63	-0.9842	0.9725	2.4031	4.7085	14.2883	0.0031	-0.2125	0.2515	0.0326	0.0984	-0.0605	-0.3875	-0.4073	-0.1015	0.2528	0.0727	0.0287	0.1733	0.038	0.2348	12.0731	53.8156	24.8122
19	3.6849	0.434	3.1808	3.6914	0.9345	7.4256	-0.0302	-0.0981	0.0478	-0.0078	0.0223	0.0904	-0.5812	-0.2966	0.0079	0.0771	0.0137	0.0396	0.1007	-0.0074	0.1406	24.0174	54.1446	21.9326
20	1.6649	-0.0611	0.9344	0.4557	-1.1658	3.3479	0.0381	-0.0395	-0.0635	-0.0354	0.1007	0.0453	0.105	-0.272	-0.1388	0.0093	0.008	-0.0275	0.1463	0.0014	0.1329	17.0586	42.7314	20.999
21	2.3831	2.8601	-1.5585	9.3165	-1.8773	2.8233	-0.0668	-0.0716	0.061	0.0582	0.0844	0.0883	-0.2349	0.0132	-0.0176	0.0501	0.0041	-0.0157	0.1138	0.0086	0.0613	26.9146	49.8846	15.2561
22	0.2488	-0.033	0.1067	2.1795	-0.1944	2.0609	0.0556	0.0117	-0.0059	-0.1765	-0.0008	0.0012	-0.0465	0.0007	-0.0549	0.0348	0.0091	-0.0189	0.1041	0.0094	0.0786	25.6266	44.0894	-10.0337
23	6.4325	3.1627	1.5771	11.3929	10.5312	22.7584	-0.0507	0.4635	-0.2788	-0.9485	0.2117	-0.4892	-0.5753	0.1425	-0.1611	0.1127	0.0079	0.0651	0.0793	0.013	0.0714	35.7195	50.0945	-18.3208
24	1.6278	-1.2366	-0.5104	3.8528	3.0037	2.5798	0.0061	-0.0137	0.1372	-0.4152	0.1364	-0.3214	-0.3189	0.1207	-0.1425	0.1462	-0.0419	0.0698	0.0773	0.0183	0.1641	33.2489	64.4729	-8.1113
25	1.8401	1.2261	-1.0693	5.4749	-0.614	3.2678	0.0541	-0.2312	-0.0104	0.0862	-0.0256	-0.406	-0.0178	0.2322	-0.0286	0.0477	-0.0122	-0.05	0.0425	-0.0131	0.0973	32.3019	69.0891	3.9071
26	0.5384	-0.8356	0.0347	2.1341	-0.0146	0.4176	0.0366	0.0013	0.0968	-0.0144	-0.0858	-0.0569	0.0404	0.0116	0.0492	0.0266	-0.0161	-0.0177	0.1163	-0.0036	0.0906	26.2089	48.2037	1.6209
27	1.1471	2.1582	1.5064	5.4953	2.9957	3.9738	0.0641	0.0352	0.105	0.0717	-0.2794	0.2382	-0.0116	-0.3048	0.2153	0.1087	0.0114	-0.0517	0.1383	-0.0194	0.0956	23.2547	66.504	0.6104
28	6.4579	-1.7589	1.5843	9.4721	-2.6651	10.326	0.2731	-0.1523	0.2146	-0.0892	-0.2075	0.1379	0.348	0.1973	-0.0655	0.1719	-0.0161	-0.0335	0.0277	-0.0264	0.0502	26.6972	75.4211	10.7972
29	5.6375	2.4976	3.0315	6.3219	0.9001	4.2399	0.266	-0.0435	0.2036	0.686	-0.2186	0.5039	-0.1798	-0.3147	-0.0474	0.1319	0.0182	0.0434	0.0487	-0.0151	0.0876	16.3252	62.9205	8.8627
30	0.164	0.2162	-0.4567	1.5141	1.8546	6.2921	-0.0084	-0.0012	0.027	-0.179	-0.093	0.146	-0.1909	-0.2551	0.1014	0.0605	0.0043	-0.0463	0.1072	0.0025	0.1154	17.3898	43.9836	-7.757

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	13 - 23
2	X-RAY DIFFRACTION	2	A	24 - 37
3	X-RAY DIFFRACTION	3	A	38 - 62
4	X-RAY DIFFRACTION	4	A	63 - 72
5	X-RAY DIFFRACTION	5	A	73 - 92
6	X-RAY DIFFRACTION	6	A	93 - 134
7	X-RAY DIFFRACTION	7	A	135 - 145
8	X-RAY DIFFRACTION	8	A	146 - 162
9	X-RAY DIFFRACTION	9	A	163 - 175
10	X-RAY DIFFRACTION	10	A	176 - 194
11	X-RAY DIFFRACTION	11	A	195 - 223
12	X-RAY DIFFRACTION	12	A	224 - 235
13	X-RAY DIFFRACTION	13	A	236 - 244
14	X-RAY DIFFRACTION	14	A	245 - 268
15	X-RAY DIFFRACTION	15	A	269 - 280
16	X-RAY DIFFRACTION	16	B	9 - 20
17	X-RAY DIFFRACTION	17	B	21 - 34
18	X-RAY DIFFRACTION	18	B	35 - 50
19	X-RAY DIFFRACTION	19	B	51 - 59
20	X-RAY DIFFRACTION	20	B	60 - 74
21	X-RAY DIFFRACTION	21	B	75 - 91
22	X-RAY DIFFRACTION	22	B	92 - 130
23	X-RAY DIFFRACTION	23	B	131 - 137
24	X-RAY DIFFRACTION	24	B	138 - 154
25	X-RAY DIFFRACTION	25	B	155 - 185
26	X-RAY DIFFRACTION	26	B	186 - 222
27	X-RAY DIFFRACTION	27	B	223 - 235
28	X-RAY DIFFRACTION	28	B	236 - 243
29	X-RAY DIFFRACTION	29	B	244 - 262
30	X-RAY DIFFRACTION	30	B	263 - 280

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Open data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi