PDB-2b0l: C-terminal DNA binding domain of transcriptional pleiotropic repr...

ID or keywords:

Entry

Database: PDB / ID: 2b0l

Title

C-terminal DNA binding domain of transcriptional pleiotropic repressor CodY.

Components

GTP-sensing transcriptional pleiotropic repressor codY

Keywords

DNA BINDING PROTEIN / CodY / DNA-binding / Nucleotide-binding / Repressor / Transcription regulation / Winged HTH motif.

Function / homology

Function and homology information

DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / GTP binding / cytoplasm
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.9 Å

Authors

Levdikov, V.M. / Blagova, E. / Joseph, P. / Sonenshein, A.L. / Wilkinson, A.J.

Citation

Journal: J.Biol.Chem. / Year: 2006
Title: The Structure of CodY, a GTP- and Isoleucine-responsive Regulator of Stationary Phase and Virulence in Gram-positive Bacteria.
Authors: Levdikov, V.M. / Blagova, E. / Joseph, P. / Sonenshein, A.L. / Wilkinson, A.J.

History

Deposition	Sep 14, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 21, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Derived calculations / Version format compliance
Revision 1.3	Oct 11, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4	Feb 14, 2024	Group: Advisory / Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2b0l.cif.gz	72.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2b0l.ent.gz	57.4 KB	Display	PDB format
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Validation report

Summary document	2b0l_validation.pdf.gz	420.9 KB	Display	wwPDB validaton report
Full document	2b0l_full_validation.pdf.gz	431.9 KB	Display
Data in XML	2b0l_validation.xml.gz	8.9 KB	Display
Data in CIF	2b0l_validation.cif.gz	12.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b0/2b0l ftp://data.pdbj.org/pub/pdb/validation_reports/b0/2b0l	HTTPS FTP

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Related structure data

Related structure data	2b18C 2gx5C 2hgvC C: citing same article (ref.)
Similar structure data	5mu3-2 1owr-4 3kxd-d 4l4i-d 5mu3-1 4ksl-3 2gzw-1 2oz6-1 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
Related items in Molecule of the Month	#183 - Mar 2015 Phototropin similarity (1) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (1)

Deposited unit

A: GTP-sensing transcriptional pleiotropic repressor codY

B: GTP-sensing transcriptional pleiotropic repressor codY

C: GTP-sensing transcriptional pleiotropic repressor codY

33.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GTP-sensing transcriptional pleiotropic repressor codY

B: GTP-sensing transcriptional pleiotropic repressor codY

A: GTP-sensing transcriptional pleiotropic repressor codY

B: GTP-sensing transcriptional pleiotropic repressor codY

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

2

C: GTP-sensing transcriptional pleiotropic repressor codY

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

Unit cell

Length a, b, c (Å)	68.128, 68.128, 164.903
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	89
Space group name H-M	P422

Details

The tetramer from A and B molecules is generated by the operation: -X, 1-Y, Z / The tetramer from C molecule is generated by the operations: -X, 1-Y, Z ; -X, Y, 1-Z ; X, 1-Y, 1-Z

#1: Protein	GTP-sensing transcriptional pleiotropic repressor codY / Vegetative protein 286B / VEG286B Mass: 11290.949 Da / Num. of mol.: 3 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: codY / Plasmid: pET-YSBLIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P39779
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

GTP-sensing transcriptional pleiotropic repressor codY / Vegetative protein 286B / VEG286B

Mass: 11290.949 Da / Num. of mol.: 3 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus subtilis (bacteria) / Gene: codY / Plasmid: pET-YSBLIC / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P39779

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.9 Å³/Da / Density % sol: 56.7 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: ammoium sulphate, sodium citrate, NaCl, glycerol, tacsimate, TRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	298	1
2	100	1
1,2		1

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
ROTATING ANODE			RIGAKU RU200	1	1.54178
SYNCHROTRON	ESRF	ID23-1		2	0.978, 0.975, 0.978

Detector

Type	ID	Detector	Date	Details
MARRESEARCH	1	IMAGE PLATE	Aug 12, 2005	Blue Osmics
ADSC QUANTUM 315r	2	CCD	Feb 12, 2005

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	MAD	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.54178	1
2	0.978	1
3	0.975	1

Reflection

Resolution: 2.9→25 Å / Num. all: 8705 / Num. obs: 8705 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / R_merge(I) obs: 0.072 / Net I/σ(I): 15.4

Reflection shell

Resolution: 2.9→2.974 Å / Redundancy: 2.4 % / R_merge(I) obs: 0.655 / Mean I/σ(I) obs: 1.2 / Num. unique all: 758 / % possible all: 84.3

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
HKL2Map		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.9→10 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.929 / SU B: 32.515 / SU ML: 0.289 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25033	393	4.7 %	RANDOM
R_work	0.20215	-	-	-
all	0.20445	8018	-	-
obs	0.20445	8018	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 74.163 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.22 Å²	0 Å²	0 Å²
2-	-	-0.22 Å²	0 Å²
3-	-	-	0.44 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→10 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2234	0	0	19	2253

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.021	2196
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.544	1.952	2948
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.702	5	292
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.888	24.318	88
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	23.582	15	399
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.915	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	339
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1599
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.268	0.2	974
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	1480
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.182	0.2	74
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	0.302	0.2	93
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.159	0.2	2
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	3.262	6	1453
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	5.127	7	2260
X-RAY DIFFRACTION	r_scbond_it	6.356	9	797
X-RAY DIFFRACTION	r_scangle_it	9.24	11	687
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.9→2.969 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.393	23	-
R_work	0.369	469	-
obs	-	469	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	65.5024	-20.2646	-68.3646	6.2693	21.15	71.3519	1.3162	-3.3279	1.4773	-3.1144	1.8901	-2.3953	-1.074	1.096	-3.2063	0.9743	-0.215	0.0712	0.2648	0.035	1.8881	16.042	39.411	20.607
2	2.3575	4.5754	0.7936	9.7076	-0.4396	5.0042	-0.6228	0.3344	-0.2561	0.0949	0.5506	-0.44	0.075	-0.4121	0.0722	0.0803	0.0741	-0.0444	-0.0185	-0.0414	0.1376	4.875	30.617	24.283
3	2.7813	0.6541	-3.5452	3.8436	-0.3153	4.5919	0.0632	-0.0725	-0.4795	0.2222	-0.2479	-0.279	-0.095	-0.1302	0.1847	0.0586	0.0097	0.0024	-0.0165	0.0078	0.2127	0.86	15.818	20.707
4	3.1518	0.3576	-1.1746	4.7658	0.2895	2.7182	-0.2245	0.0865	-0.406	-0.7265	0.1161	-0.2431	0.3647	-0.1065	0.1084	0.1024	-0.0137	0.0801	-0.0258	-0.0108	0.2098	2.042	13.129	10.068
5	10.879	12.3885	8.5145	17.114	0.4603	35.0327	-0.3125	1.1367	0.2411	0.4259	0.1192	1.521	0.7577	-0.1864	0.1933	-0.0563	0.0042	-0.0437	-0.0033	-0.1199	0.3843	-8.743	11.771	15.444
6	19.1402	3.2637	-10.8583	24.6192	13.3249	15.7318	0.3605	0.1161	-0.0056	0.3609	-0.0921	0.0889	-0.3239	-0.7322	-0.2684	0.0087	0	-0.0925	0.0046	0.0571	0.0924	-6.826	19.557	15.9
7	5.3031	2.0158	-2.6341	14.8871	-2.5093	1.4695	0.1116	0.1056	0.3321	0.073	-0.1787	-0.2095	-0.4007	0.2562	0.0671	0.0225	0.0172	-0.0113	0.0442	0.0261	0.1302	-2.711	27.15	14.83
8	7.7395	-0.8364	-7.9477	40.235	1.8357	8.1853	0.3041	0.1475	0.4045	-1.2826	-0.4148	2.1593	-1.2553	-2.1643	0.1107	0.2058	0.0512	-0.2074	0.2003	0.0773	0.026	-4.775	19.665	2.03
9	4.0983	2.3641	9.1775	11.871	3.867	20.7452	-0.0455	0.0179	-0.2244	-0.5004	0.4513	-1.0879	-0.5701	0.6544	-0.4058	0.0799	-0.0267	0.1146	-0.0416	-0.0881	0.226	4.717	28.16	11.111
10	2.0971	-4.8192	-2.2462	18.2602	-3.9026	13.8411	-0.7035	-0.2551	-0.1249	0.0531	0.2852	-1.4422	0.2607	0.2896	0.4183	-0.0786	0.0732	-0.0198	0.085	-0.0027	0.418	10.437	21.767	20.418
11	220.7551	125.4974	22.1819	208.079	97.1908	54.5483	-2.9994	-3.2346	0.0035	3.0597	3.2108	-0.854	-3.5903	-2.9039	-0.2114	0.473	0.1553	0.1092	0.367	0.3839	0.1629	-2.215	48.168	33.806
12	1.4901	2.995	-0.9369	15.0423	-2.6767	0.6589	0.1522	0.4161	0.2208	0.4828	-0.1291	0.6816	0.0842	-0.4229	-0.0231	0.0697	-0.0448	0.1284	0.1729	0.1202	0.0969	-5.671	36.156	30.957
13	3.0908	-1.9493	4.7324	11.8067	-0.0887	9.0822	0.43	0.967	0.2387	0.0041	-0.8096	0.9773	1.0127	-1.1902	0.3796	-0.1742	-0.1004	0.0342	0.3175	-0.1171	0.0479	-15.189	24.162	34.161
14	5.6271	3.0238	4.485	15.3387	4.1877	6.9109	0.5503	-0.7366	-0.1095	0.9566	-0.8383	1.3847	0.2424	-1.4606	0.288	0.1972	-0.3069	0.2331	0.1687	-0.1134	-0.0206	-18.496	23.062	45.263
15	27.0421	-19.5144	-21.4026	18.4814	11.6329	20.2423	-1.3285	-2.6507	-2.9867	0.1144	0.0928	-3.6835	-0.2243	2.3927	1.2357	0.3908	-0.2819	0.0562	-0.0065	-0.0023	0.5525	-12.959	13.889	39.053
16	32.9293	23.0174	0.0309	16.381	-2.7664	26.6264	0.966	-0.3752	-1.2143	1.351	-1.5942	-1.2042	1.2325	0.6227	0.6282	0.1918	-0.1252	-0.0255	-0.0274	0.0395	0.0748	-8.009	19.883	39.413
17	5.6084	-5.9875	1.1995	8.1771	3.1869	11.4387	-0.13	0.3594	0.1818	0.7635	0.3165	-0.6984	-0.4721	0.3307	-0.1865	0.1452	-0.062	0.0277	0.0313	0.0248	-0.0254	-4.236	27.858	40.595
18	6.193	-1.844	11.097	1.3916	-6.8562	34.859	-0.6222	0.3688	-2.2187	-2.745	1.6704	-5.0669	1.0551	3.6286	-1.0482	0.8094	-0.0192	-0.0438	0.3696	0.1478	0.3999	-8.26	21.229	52.863
19	5.0712	-0.4384	-5.796	18.5606	-1.7976	11.0014	-0.6576	0.3746	0.425	0.0114	0.4957	-1.6501	-0.9384	-1.8419	0.1619	0.3756	-0.2615	0.2637	-0.0078	-0.1571	0.0268	-7.747	34.421	44.166
20	73.2612	10.9224	-39.1488	37.1886	0.2804	21.9723	1.9112	1.408	0.5746	0.424	-2.149	0.1677	-0.8826	-1.4962	0.2378	-0.0008	0.4233	0.3444	0.5367	0.2111	0.0515	-15.042	36.427	34.891
21	39.9413	24.5406	-104.6529	71.2476	-2.1631	342.9482	-5.2222	3.1382	6.4116	7.4523	0.2707	-7.0143	7.7655	5.3556	4.9515	1.0078	0.3173	-0.131	0.8242	0.1649	0.4739	11.7	24.135	76.538
22	51.2327	15.6413	-16.8342	29.2949	-8.4755	30.6125	-1.9258	1.4726	-0.5524	0.3528	0.4729	-0.4381	-1.6444	0.718	1.4529	0.6663	-0.2133	-0.0078	0.1999	-0.0038	-0.8615	-0.805	28.622	78.913
23	2.6549	-4.4806	3.0615	16.4705	7.1974	20.6903	0.3418	-1.2531	-1.9831	1.3819	1.0764	0.1022	-0.2401	3.3117	-1.4182	0.4227	-0.2986	0.1935	1.0849	0.0304	-0.5037	-16.161	26.024	75.748
24	0.9701	2.9867	1.6293	9.1948	5.016	2.7363	-0.5289	-0.1528	-2.7691	0.09	0.0059	0.292	0.2213	-0.5451	0.5229	0.4049	0.052	0.1947	1.0152	0.2105	0.0492	-18.072	23.32	64.616
25	77.6882	48.7999	-57.4676	148.7848	62.4499	124.7217	-3.5525	5.7359	-0.4279	-0.4608	-4.4373	8.0443	0.0013	-6.4053	7.9898	0.8062	0.5029	-0.3434	1.2871	0.6776	-0.1703	-22.77	33.035	69.332
26	163.9437	26.2365	-24.2371	97.896	45.7367	29.856	0.1108	-6.7103	-3.9396	-4.1553	-0.1058	-0.7406	0.7251	1.9949	-0.005	0.779	-0.0602	-0.0614	0.5286	0.2104	-1.0491	-15.954	34.429	70.484
27	1.9142	6.3902	1.8561	32.2766	7.0404	1.8649	-0.1754	-0.0991	0.8537	0.5772	0.681	-0.3081	-1.3339	0.0668	-0.5057	0.1619	-0.1164	0.0096	1.2331	0.0028	-0.5569	-7.287	33.58	68.763
28	31.6426	27.6852	1.6525	24.2358	1.0655	11.1266	0.625	0.1255	2.4522	0.1987	-1.2781	1.9276	-1.6485	0.5708	0.6532	0.2974	0.1207	0.1161	0.4268	-0.1512	-0.548	-16.034	32.972	56.713
29	18.2491	41.7174	6.5684	95.3659	15.0153	2.3642	-6.3569	-1.7461	1.8002	0.2253	2.0179	-4.1277	-2.7569	-0.7025	4.3389	1.2424	0.1175	-0.0933	0.8888	-0.0757	-0.7019	-2.598	27.138	66.594
30	36.5637	30.7136	60.1628	25.7996	50.5369	98.9932	-0.0025	-9.3279	2.0945	-5.421	-1.5174	1.8877	5.4014	6.4357	1.5199	0.4976	0.3295	0.4653	0.2566	0.35	0.8361	-5.571	19.406	75.544

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	161 - 165	4 - 8
2	X-RAY DIFFRACTION	2	A	A	166 - 177	9 - 20
3	X-RAY DIFFRACTION	3	A	A	178 - 191	21 - 34
4	X-RAY DIFFRACTION	4	A	A	192 - 212	35 - 55
5	X-RAY DIFFRACTION	5	A	A	213 - 216	56 - 59
6	X-RAY DIFFRACTION	6	A	A	217 - 222	60 - 65
7	X-RAY DIFFRACTION	7	A	A	223 - 232	66 - 75
8	X-RAY DIFFRACTION	8	A	A	233 - 241	76 - 84
9	X-RAY DIFFRACTION	9	A	A	242 - 247	85 - 90
10	X-RAY DIFFRACTION	10	A	A	248 - 258	91 - 101
11	X-RAY DIFFRACTION	11	B	B	163 - 165	6 - 8
12	X-RAY DIFFRACTION	12	B	B	166 - 177	9 - 20
13	X-RAY DIFFRACTION	13	B	B	178 - 191	21 - 34
14	X-RAY DIFFRACTION	14	B	B	192 - 212	35 - 55
15	X-RAY DIFFRACTION	15	B	B	213 - 216	56 - 59
16	X-RAY DIFFRACTION	16	B	B	217 - 222	60 - 65
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