PDB-5c8d: Crystal structure of full-length Thermus thermophilus CarH bound ...

ID or keywords:

Entry

Database: PDB / ID: 5c8d

Title

Crystal structure of full-length Thermus thermophilus CarH bound to adenosylcobalamin (dark state)

Components

Light-dependent transcriptional regulator CarH

Keywords

TRANSCRIPTIONAL REGULATOR / Transcription factor / light sensor / adenosylcobalamin-binding / DNA-binding

Function / homology

Function and homology information

cobalamin binding / DNA-binding transcription factor activity / DNA binding / identical protein binding / metal ion binding
Similarity search - Function

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Jost, M. / Drennan, C.L.

Funding support

United States, 2items

Citation

Journal: Nature / Year: 2015
Title: Structural basis for gene regulation by a B12-dependent photoreceptor.
Authors: Jost, M. / Fernandez-Zapata, J. / Polanco, M.C. / Ortiz-Guerrero, J.M. / Chen, P.Y. / Kang, G. / Padmanabhan, S. / Elias-Arnanz, M. / Drennan, C.L.

History

Deposition	Jun 25, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 30, 2015	Provider: repository / Type: Initial release
Revision 1.1	Oct 14, 2015	Group: Database references
Revision 1.2	Nov 4, 2015	Group: Database references
Revision 1.3	Sep 20, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Nov 20, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Mar 6, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5c8d.cif.gz	796.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5c8d.ent.gz	658.7 KB	Display	PDB format
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Validation report

Summary document	5c8d_validation.pdf.gz	4.6 MB	Display	wwPDB validaton report
Full document	5c8d_full_validation.pdf.gz	4.8 MB	Display
Data in XML	5c8d_validation.xml.gz	72.5 KB	Display
Data in CIF	5c8d_validation.cif.gz	91.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c8/5c8d ftp://data.pdbj.org/pub/pdb/validation_reports/c8/5c8d	HTTPS FTP

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Related structure data

Related structure data	5c8aC 5c8eC 5c8fC C: citing same article (ref.)
Similar structure data	4rxo-2 6dww-d 4rxo-1 4q15-d 6koe-2 5xih-1 6dx0-d 6u6x-1 1h4t-2 5xiq-2 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
Related items in Molecule of the Month	#16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1)

Deposited unit

A: Light-dependent transcriptional regulator CarH

B: Light-dependent transcriptional regulator CarH

C: Light-dependent transcriptional regulator CarH

D: Light-dependent transcriptional regulator CarH

E: Light-dependent transcriptional regulator CarH

F: Light-dependent transcriptional regulator CarH

G: Light-dependent transcriptional regulator CarH

H: Light-dependent transcriptional regulator CarH

hetero molecules

279 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Light-dependent transcriptional regulator CarH

B: Light-dependent transcriptional regulator CarH

C: Light-dependent transcriptional regulator CarH

D: Light-dependent transcriptional regulator CarH

hetero molecules

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

2

E: Light-dependent transcriptional regulator CarH

F: Light-dependent transcriptional regulator CarH

G: Light-dependent transcriptional regulator CarH

H: Light-dependent transcriptional regulator CarH

hetero molecules

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

Unit cell

Length a, b, c (Å)	78.740, 79.720, 118.450
Angle α, β, γ (deg.)	90.73, 96.61, 117.29
Int Tables number	1
Space group name H-M	P1

#1: Protein	Light-dependent transcriptional regulator CarH Mass: 33323.250 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_P0056 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star pLysS / References: UniProt: Q746J7
#2: Chemical	ChemComp-B12 / COBALAMIN Mass: 1330.356 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₆₂H₈₉CoN₁₃O₁₄P
#3: Chemical	ChemComp-5AD / 5'-DEOXYADENOSINE Mass: 251.242 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₃

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.6 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 3350, 0.1 M ammonium citrate tribasic pH 7

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 23, 2013
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.8→100 Å / Num. obs: 59284 / % possible obs: 94.9 % / Redundancy: 5.6 % / B_iso Wilson estimate: 61 Å² / R_sym value: 0.105 / Net I/σ(I): 12
Reflection shell	Resolution: 2.8→2.87 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2 / % possible all: 95.5

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: two starting models were used for MR. One model contained residues 80-270 of CarH, determined by Co-SAD.

Resolution: 2.8→70.65 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / Phase error: 27.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23	3027	5.11 %	Random selection
R_work	0.183	-	-	-
obs	0.186	59232	94.8 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 75.9 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→70.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14668	0	872	0	15540

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	15981
X-RAY DIFFRACTION	f_angle_d	0.921	21964
X-RAY DIFFRACTION	f_dihedral_angle_d	11.252	6019
X-RAY DIFFRACTION	f_chiral_restr	0.036	2486
X-RAY DIFFRACTION	f_plane_restr	0.005	3141

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 (%)
2.8001-2.8438	0.3555	151	0.3161	2582	X-RAY DIFFRACTION	95
2.8438-2.8904	0.3392	135	0.2896	2565	X-RAY DIFFRACTION	96
2.8904-2.9403	0.3009	148	0.2789	2585	X-RAY DIFFRACTION	95
2.9403-2.9937	0.3358	143	0.2723	2483	X-RAY DIFFRACTION	94
2.9937-3.0513	0.2954	126	0.2631	2575	X-RAY DIFFRACTION	93
3.0513-3.1136	0.3081	122	0.2522	2466	X-RAY DIFFRACTION	93
3.1136-3.1813	0.3308	146	0.257	2629	X-RAY DIFFRACTION	97
3.1813-3.2553	0.3174	138	0.2505	2568	X-RAY DIFFRACTION	96
3.2553-3.3367	0.3007	144	0.237	2570	X-RAY DIFFRACTION	96
3.3367-3.4269	0.2921	140	0.2134	2603	X-RAY DIFFRACTION	96
3.4269-3.5278	0.2633	125	0.1952	2537	X-RAY DIFFRACTION	95
3.5278-3.6416	0.2492	113	0.1828	2597	X-RAY DIFFRACTION	94
3.6416-3.7718	0.2193	150	0.1799	2473	X-RAY DIFFRACTION	92
3.7718-3.9228	0.2202	121	0.1727	2564	X-RAY DIFFRACTION	95
3.9228-4.1013	0.2074	132	0.1625	2579	X-RAY DIFFRACTION	96
4.1013-4.3175	0.1919	148	0.148	2581	X-RAY DIFFRACTION	96
4.3175-4.588	0.1859	151	0.1419	2552	X-RAY DIFFRACTION	95
4.588-4.9421	0.1928	139	0.1459	2503	X-RAY DIFFRACTION	93
4.9421-5.4393	0.22	144	0.1676	2553	X-RAY DIFFRACTION	95
5.4393-6.226	0.2269	126	0.1828	2605	X-RAY DIFFRACTION	96
6.226-7.8424	0.217	128	0.1638	2500	X-RAY DIFFRACTION	92
7.8424-70.6747	0.1597	157	0.1394	2535	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	2.6632	0.1276	-0.4571	1.7587	-0.5969	2.0198	0.0656	0.0829	-0.1453	-0.1624	-0.1739	-0.0409	0.0851	0.1438	0.1272	0.7709	0.1384	-0.0362	0.4847	0.0447	0.4437	-30.5387	5.0482	-7.2341
2	2.5125	-0.5573	0.3496	0.7441	-0.6677	1.8779	0.0542	-0.3075	0.1095	0.5967	0.0403	-0.0073	-0.3579	-0.1745	-0.1271	0.909	0.1338	-0.0113	0.5435	0.0114	0.4612	-35.5765	22.75	6.3236
3	2.5677	-1.14	-0.4676	2.2321	-0.9012	2.7892	0.0498	-0.1468	0.1234	0.2302	-0.1451	-0.089	-0.3836	0.2263	0.117	0.7953	0.0619	0.0151	0.5939	0.1061	0.5029	-23.3709	-5.6702	22.0414
4	4.9801	-0.572	1.5798	4.256	-1.6074	5.3429	0.1508	-0.2473	-0.102	0.3966	0.0032	0.303	0.0604	-0.2396	-0.1403	0.4321	0.0548	-0.0512	0.3903	-0.0516	0.3449	-31.2992	-12.8851	-30.1085
5	2.1881	0.4598	-1.7299	1.7892	-1.647	5.3095	0.0951	0.2094	-0.1322	-0.3505	0.0093	0.155	0.2506	-0.3331	-0.0882	0.7916	0.1138	-0.0193	0.5828	-0.0188	0.4648	-33.4546	-24.9064	15.8593
6	8.2547	0.9728	0.455	5.0629	1.6131	0.6243	0.545	0.3956	0.0492	-0.6717	0.1083	-0.0493	0.3469	-0.2335	-0.5258	0.4819	-0.0477	-0.1402	0.6028	0.105	0.4403	28.5344	-10.5437	-46.5834
7	4.1134	-0.2677	0.6603	2.0654	-1.0407	2.7733	0.0341	0.0054	0.0997	-0.0626	-0.0538	-0.1012	-0.1308	-0.1045	0.0164	0.5748	0.1009	0.0128	0.4399	0.0225	0.3614	-11.6587	-13.2043	-58.0001
8	3.1972	1.1412	1.4161	6.7156	-0.6458	5.0987	-0.0978	-0.1134	0.3411	0.0064	-0.17	-0.5292	-0.2899	0.3978	0.2995	0.7204	0.0307	0.0552	0.6708	0.1922	0.9852	-6.3414	-59.5173	-51.4913
9	2.6292	0.5805	-0.3927	1.8614	-1.8682	2.5128	0.1621	0.2187	-0.1853	-0.3664	-0.2737	-0.1527	0.7816	0.4446	0.1235	0.9528	0.2388	0.055	0.71	0.0524	0.5048	-2.1286	-29.6206	-71.1713
10	2.8882	2.312	-0.2001	1.9307	0.3055	3.175	0.2448	0.5783	-0.4602	-0.3328	0.0657	-0.3643	0.2732	0.7771	-0.3411	1.1209	0.5119	0.0036	1.099	0.1269	1.0268	24.7649	-41.1185	-56.9071
11	3.2903	-0.6347	-0.7696	2.1439	-1.0157	3.1794	-0.0409	-0.0268	-0.2439	-0.1264	0.0021	0.1293	0.383	0.1144	0.0376	0.5903	0.0756	-0.0483	0.4905	0.046	0.4251	-8.3193	-36.4974	-32.3247
12	0.7694	-0.2343	-2.155	4.6469	-1.3224	6.9348	0.023	-0.4244	0.2612	0.3976	0.7096	0.289	-1.0764	-0.5731	-0.8584	1.1856	0.093	-0.1496	1.057	0.1363	1.3509	2.8498	9.333	-45.583
13	3.4966	-1.5239	1.7057	2.2788	-1.3798	3.5495	0.0514	-0.1399	0.3633	0.321	-0.1886	-0.3162	-0.2538	0.1832	0.1347	0.4964	-0.0312	-0.0329	0.466	0.0882	0.5946	6.1044	-21.9508	-22.7307

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'A' )
2	X-RAY DIFFRACTION	2	(chain 'B' )
3	X-RAY DIFFRACTION	3	(chain 'C' )
4	X-RAY DIFFRACTION	4	(chain 'D' and resid 4 through 80)
5	X-RAY DIFFRACTION	5	(chain 'D' and resid 81 through 301)
6	X-RAY DIFFRACTION	6	(chain 'E' and resid 4 through 80)
7	X-RAY DIFFRACTION	7	(chain 'E' and resid 81 through 301)
8	X-RAY DIFFRACTION	8	(chain 'F' and resid 5 through 80)
9	X-RAY DIFFRACTION	9	(chain 'F' and resid 81 through 301)
10	X-RAY DIFFRACTION	10	(chain 'G' and resid 4 through 80)
11	X-RAY DIFFRACTION	11	(chain 'G' and resid 81 through 301)
12	X-RAY DIFFRACTION	12	(chain 'H' and resid -6 through 80)
13	X-RAY DIFFRACTION	13	(chain 'H' and resid 81 through 301)

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