PDB-4c97: Cas6 (TTHA0078) H37A mutant

ID or keywords:

Entry

Database: PDB / ID: 4c97

Title

Cas6 (TTHA0078) H37A mutant

Components

CAS6A

Keywords

HYDROLASE / CRISPR CAS PROTEIN RNA PROCESSING RIBONUCLEASE

Function / homology

Function and homology information

endonuclease activity / defense response to virus
Similarity search - Function

Biological species

THERMUS THERMOPHILUS HB8 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Jinek, M. / Niewoehner, O. / Doudna, J.A.

Citation

Journal: Nucleic Acids Res. / Year: 2014
Title: Evolution of Crispr RNA Recognition and Processing by Cas6 Endonucleases.
Authors: Niewoehner, O. / Jinek, M. / Doudna, J.A.

History

Deposition	Oct 2, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 6, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2013	Group: Atomic model / Other
Revision 1.2	Feb 12, 2014	Group: Database references
Revision 1.3	Jul 23, 2014	Group: Atomic model / Other
Revision 1.4	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4c97.cif.gz	282.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4c97.ent.gz	234.4 KB	Display	PDB format
PDBx/mmJSON format	4c97.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c9/4c97 ftp://data.pdbj.org/pub/pdb/validation_reports/c9/4c97	HTTPS FTP

-
Related structure data

Related structure data	4c8ySC 4c8zC 4c98C 4c9dC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4m6b-1 4ds3-d 5tss-2 5mkc-2 1aw7-2 4k85-4 4wml-d 1dy6-2 6qwa-d 1cz4-d 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: CAS6A

B: CAS6A

hetero molecules

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

1

A: CAS6A

hetero molecules

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

2

B: CAS6A

hetero molecules

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

Unit cell

Length a, b, c (Å)	73.930, 77.450, 88.790
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	CAS6A Mass: 26513.404 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS HB8 (bacteria) / Plasmid: PEC-K-MBP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q5SM65
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.3 % / Description: NONE
Crystal grow	pH: 6.5 Details: 0.1M BIS-TRIS PROPANE (PH 6.5), 16% PEG 335, 0.2 M SODIUM SULFATE

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979023
Detector	Type: ADSC CCD / Detector: CCD / Date: Apr 4, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979023 Å / Relative weight: 1
Reflection	Resolution: 1.7→58.4 Å / Num. obs: 56542 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / R_merge(I) obs: 0.08 / Net I/σ(I): 13.4
Reflection shell	Resolution: 1.7→1.74 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.73 / Mean I/σ(I) obs: 2 / % possible all: 99.7

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.8.2_1309)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C8Y

4c8y

Resolution: 1.7→58.366 Å / SU ML: 0.17 / σ(F): 2 / Phase error: 19.32 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1912	2835	5 %
R_work	0.1679	-	-
obs	0.169	56486	99.59 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.7→58.366 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3631	0	20	414	4065

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	3788
X-RAY DIFFRACTION	f_angle_d	1.349	5146
X-RAY DIFFRACTION	f_dihedral_angle_d	12.449	1419
X-RAY DIFFRACTION	f_chiral_restr	0.071	549
X-RAY DIFFRACTION	f_plane_restr	0.007	675

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 (%)
1.7004-1.7297	0.266	134	0.2411	2594	X-RAY DIFFRACTION	98
1.7297-1.7611	0.2188	144	0.2307	2668	X-RAY DIFFRACTION	100
1.7611-1.795	0.238	138	0.2077	2623	X-RAY DIFFRACTION	100
1.795-1.8316	0.2403	143	0.2066	2659	X-RAY DIFFRACTION	100
1.8316-1.8715	0.2423	137	0.1958	2670	X-RAY DIFFRACTION	100
1.8715-1.915	0.2027	138	0.1792	2649	X-RAY DIFFRACTION	100
1.915-1.9629	0.2088	146	0.1697	2680	X-RAY DIFFRACTION	100
1.9629-2.016	0.1841	142	0.1629	2646	X-RAY DIFFRACTION	100
2.016-2.0753	0.1825	142	0.1595	2676	X-RAY DIFFRACTION	100
2.0753-2.1423	0.1993	139	0.1582	2678	X-RAY DIFFRACTION	100
2.1423-2.2189	0.1767	137	0.1507	2672	X-RAY DIFFRACTION	100
2.2189-2.3077	0.1708	150	0.1487	2660	X-RAY DIFFRACTION	100
2.3077-2.4127	0.1614	138	0.1472	2705	X-RAY DIFFRACTION	100
2.4127-2.5399	0.1709	146	0.1506	2668	X-RAY DIFFRACTION	100
2.5399-2.6991	0.1821	139	0.1566	2693	X-RAY DIFFRACTION	100
2.6991-2.9075	0.2125	144	0.1611	2693	X-RAY DIFFRACTION	100
2.9075-3.2	0.1912	142	0.1705	2720	X-RAY DIFFRACTION	100
3.2-3.663	0.1925	146	0.1639	2721	X-RAY DIFFRACTION	100
3.663-4.6147	0.1605	145	0.1507	2777	X-RAY DIFFRACTION	100
4.6147-58.4	0.2037	145	0.1874	2799	X-RAY DIFFRACTION	97

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	3.4376	0.1216	0.228	1.3172	-0.3413	2.3202	0.0348	-0.3179	-0.3074	0.1426	-0.0341	0.0552	0.161	-0.0432	0.0295	0.1743	0.0233	0.0083	0.156	0.0305	0.1462	-31.9723	-9.936	14.0262
2	3.5398	0.8085	-0.0269	1.8662	-0.7601	2.2676	0.0003	-0.4107	0.0831	0.1396	0.0333	0.0713	0.0099	-0.0986	-0.0281	0.1421	0.0041	-0.0013	0.1522	0.0178	0.1166	-36.0451	-4.4346	14.4102
3	2.6816	-0.1777	1.0034	1.6029	-0.0069	1.188	0.0262	-0.6554	-0.2045	0.4599	-0.0136	-0.0572	-0.1179	0.2262	-0.0679	0.3328	-0.0178	-0.0027	0.4662	0.0613	0.1712	-31.5625	-6.7573	22.5735
4	2.2789	0.1596	-1.1369	0.6594	0.132	2.1417	0.0399	-0.5424	-0.5042	0.237	0.0036	-0.0515	0.2278	0.2551	-0.0763	0.2446	0.0347	-0.0075	0.1777	0.1014	0.2286	-29.9438	-14.4114	14.9769
5	1.7138	0.4543	0.6111	0.3975	-0.1858	1.0938	-0.0551	-0.0395	0.1026	-0.0035	0.0008	-0.0073	-0.0121	-0.0205	0.021	0.107	0.0201	0.0012	0.0867	-0.0088	0.112	-28.8002	1.387	-2.4257
6	1.5854	-0.092	-0.4261	2.0051	0.2266	2.5891	0.0308	0.062	0.1987	0.022	-0.1122	-0.1638	-0.173	-0.0186	0.0339	0.1171	-0.0024	-0.0095	0.0918	0.0319	0.1464	-26.9642	11.2053	-1.752
7	1.8849	0.6271	-1.0432	1.8632	0.1023	3.0493	-0.159	0.4374	-0.0198	0.0533	0.1182	0.1084	0.2365	-0.4414	0.1116	0.109	0.0078	-0.0229	0.1432	0.0195	0.0923	-39.525	-4.0245	-6.9396
8	2.0148	0.4967	-0.2158	1.2317	-0.2929	0.9476	-0.0385	0.1064	-0.0308	-0.0154	-0.0087	-0.1084	0.0462	0.0592	0.0146	0.0879	0.0117	0.0011	0.0799	0.0038	0.0818	-26.1743	0.6402	-2.8052
9	2.5347	-0.165	-0.1099	1.8299	-0.4117	1.7592	-0.0543	0.0801	0.0816	-0.0641	-0.0181	0.0473	-0.0055	0.029	0.0159	0.1497	-0.0248	-0.0111	0.1149	-0.0067	0.1147	-68.6124	9.3023	3.3831
10	4.6407	-1.2075	-2.106	4.183	1.3127	4.7767	0.2728	0.6385	-0.312	-0.1999	-0.0519	-0.2374	0.2767	-0.1908	0.0639	0.1619	0.0026	-0.0437	0.1984	-0.0391	0.1793	-76.6572	1.2746	-1.69
11	2.2282	-0.8015	-0.0564	2.1803	-0.3584	2.1811	0.0079	0.0603	-0.1908	-0.0398	-0.0243	0.1183	0.096	-0.0727	0.0327	0.1256	-0.0238	0.0108	0.1112	0.0157	0.1207	-70.5305	5.0892	5.8184
12	1.9443	0.0226	-0.8022	1.3631	0.2217	1.0718	-0.0394	0.2696	-0.0828	-0.4721	0.1312	-0.017	0.1725	0.2283	-0.0098	0.2662	-0.0215	0.0098	0.3092	-0.0061	0.1594	-68.5648	5.8216	-5.134
13	3.7504	0.4842	0.1709	0.8568	-0.3279	2.1961	-0.0617	0.1283	0.0734	-0.0999	-0.055	-0.0331	-0.0494	0.2377	0.0731	0.1509	-0.018	0.0012	0.0616	0.024	0.1082	-66.4642	13.5839	2.4328
14	1.3897	0.2967	-1.0023	1.1992	-0.1753	0.7318	-0.0647	-0.2334	-0.2128	0.0313	-0.1079	-0.0823	0.0151	0.009	0.0947	0.1197	0.0165	0.0278	0.1972	0.0613	0.1936	-53.127	-2.5558	14.4894
15	3.0327	-0.2394	0.3887	1.3957	-0.8024	2.584	0.037	-0.1583	-0.2125	-0.0417	-0.0043	0.2048	0.2072	0.0956	-0.0061	0.1284	0.0016	0.0065	0.123	0.0122	0.1037	-74.1572	-1.8436	22.7092
16	1.2532	-0.0964	-1.9803	0.265	0.0862	3.9775	-0.1303	-0.188	-0.3539	-0.0167	-0.0219	0.0522	0.528	-0.0783	0.0147	0.1647	0.02	0.0331	0.1745	0.0485	0.2047	-66.7037	-9.019	17.6221
17	1.214	0.5133	-0.5694	1.1008	0.3715	3.2833	0.3116	-0.3461	-0.7813	0.1467	0.0656	-0.2036	0.8188	-0.5511	0.2868	0.2741	0.0029	-0.0256	0.3384	0.2035	0.4518	-60.3046	-14.8603	22.0204
18	2.9377	-0.2679	1.3953	1.7554	0.3453	3.3248	-0.2327	-0.5656	0.0511	0.0124	0.0402	0.0947	-0.1766	-0.227	0.1442	0.0945	-0.0021	0.0175	0.198	0.0537	0.0783	-76.4181	3.7052	24.3921
19	2.7389	-1.0789	0.4542	1.3087	0.0386	0.8252	-0.0698	-0.7605	-0.1459	0.1716	0.0099	-0.0436	-0.0056	0.3584	-0.2621	0.1265	0.0112	-0.0071	0.3539	0.131	0.0988	-63.4776	-0.9487	28.3635
20	1.9558	-0.8298	0.4117	1.6573	-0.888	1.1883	-0.0385	-0.1717	-0.0686	-0.0211	-0.0757	-0.1686	0.0415	0.1549	0.0544	0.1082	-0.0029	0.0101	0.1301	0.0367	0.1094	-63.3188	-1.3489	16.6787

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 0 THROUGH 17 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 18 THROUGH 63 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 64 THROUGH 85 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 86 THROUGH 101 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 102 THROUGH 139 )
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 140 THROUGH 170 )
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESID 171 THROUGH 189 )
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESID 190 THROUGH 239 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 0 THROUGH 17 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 18 THROUGH 32 )
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 33 THROUGH 63 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 64 THROUGH 85 )
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 86 THROUGH 101 )
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESID 102 THROUGH 116 )
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESID 117 THROUGH 139 )
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESID 140 THROUGH 154 )
17	X-RAY DIFFRACTION	17	CHAIN B AND (RESID 155 THROUGH 170 )
18	X-RAY DIFFRACTION	18	CHAIN B AND (RESID 171 THROUGH 189 )
19	X-RAY DIFFRACTION	19	CHAIN B AND (RESID 190 THROUGH 204 )
20	X-RAY DIFFRACTION	20	CHAIN B AND (RESID 205 THROUGH 238 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi