PDB-3f0c: Crystal structure of transcriptional regulator from Cytophaga hut...

ID or keywords:

Entry

Database: PDB / ID: 3f0c

Title

Crystal structure of transcriptional regulator from Cytophaga hutchinsonii ATCC 33406

Components

Transcriptional regulator

Keywords

transcription regulator / TETR / MCSG / PSI / SAD / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics / DNA-binding / Transcription / Transcription regulation

Function / homology

Function and homology information

Biological species

Cytophaga hutchinsonii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.96 Å

Authors

Nocek, B. / Maltseva, N. / Tan, K. / Abdullah, J. / Eschenfeldt, W. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of transcriptional regulator from Cytophaga hutchinsonii ATCC 33406
Authors: Nocek, B. / Maltseva, N. / Tan, K. / Abdullah, J. / Stols, L. / Eschenfeldt, W. / Joachimiak, A.

History

Deposition	Oct 24, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 11, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Dec 27, 2023	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3f0c.cif.gz	52.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3f0c_validation.pdf.gz	440 KB	Display	wwPDB validaton report
Full document	3f0c_full_validation.pdf.gz	448.3 KB	Display
Data in XML	3f0c_validation.xml.gz	10.3 KB	Display
Data in CIF	3f0c_validation.cif.gz	12.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f0/3f0c ftp://data.pdbj.org/pub/pdb/validation_reports/f0/3f0c	HTTPS FTP

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Related structure data

Similar structure data	1j10-2 5m4y-2 3jrh-d 6o6n-1 3vd8-d 1ngm-1 3dgc-2 6oq6-d 1ngm-2 4ont-2 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
Other databases	TargetDB: apc88832

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Transcriptional regulator

hetero molecules

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

1

A: Transcriptional regulator

hetero molecules

A: Transcriptional regulator

hetero molecules

defined by author&software
51.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	116.099, 116.099, 46.367
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Details

likely-dimer

#1: Protein	Transcriptional regulator / TetR-molecule A Mass: 25516.377 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cytophaga hutchinsonii (bacteria) / Strain: ATCC 33406 / Gene: ycdC, CHU_0940 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q11WJ7, UniProt: A0A6N4SPM4*PLUS
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.54 Å³/Da / Density % sol: 65.21 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.0 Ammonium sulfate, 0.1M Hepes, 0.5% Pag 8000, pH 7.0 , VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2008 / 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: 2.95→40 Å / Num. all: 7735 / Num. obs: 7695 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.4 % / B_iso Wilson estimate: 86.3 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 25
Reflection shell	Resolution: 2.95→3 Å / Redundancy: 8.6 % / R_merge(I) obs: 0.591 / Mean I/σ(I) obs: 3.8 / Num. unique all: 362 / % possible all: 100

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Processing

Software

Name	Version	Classification
SBC-Collect	Collect	data collection
HKL-3000		phasing
SHELX		model building
Coot		model building
MLPHARE		phasing
DM		model building
REFMAC	5.5.0054	refinement
HKL-3000		data reduction
HKL-3000		data scaling
SHELX		phasing
DM		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.96→40 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.908 / SU B: 35.724 / SU ML: 0.291 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.73 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27083	350	4.6 %	RANDOM
R_work	0.20883	-	-	-
all	0.22	7685	-	-
obs	0.21046	7335	99.42 %	-

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: 32.875 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.4 Å²	-0.7 Å²	0 Å²
2-	-	-1.4 Å²	0 Å²
3-	-	-	2.09 Å²

Refinement step

Cycle: LAST / Resolution: 2.96→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1536	0	10	0	1546

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	1574
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1085
X-RAY DIFFRACTION	r_angle_refined_deg	1.844	1.974	2108
X-RAY DIFFRACTION	r_angle_other_deg	1.002	3	2657
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.146	5	191
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.697	24.857	70
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.617	15	305
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.979	15	5
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	233
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1705
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	316
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	0.698	1.5	955
X-RAY DIFFRACTION	r_mcbond_other	0.102	1.5	393
X-RAY DIFFRACTION	r_mcangle_it	1.415	2	1523
X-RAY DIFFRACTION	r_scbond_it	2.051	3	619
X-RAY DIFFRACTION	r_scangle_it	3.402	4.5	585
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.955→3.032 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.269	26	-
R_work	0.274	527	-
obs	-	-	99.82 %

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	15.2576	-8.3564	3.8566	18.3122	-0.8146	7.8195	-0.4123	0.7139	0.3481	-0.2435	0.0596	-1.3315	0.0673	0.6674	0.3527	0.6014	0.1919	-0.0574	0.416	0.0965	0.6633	41.108	36.27	-1.763
2	16.2442	-5.0732	4.1191	15.1964	0.9433	7.9242	-1.0226	-0.7297	-0.2789	0.8629	0.6464	1.8159	-0.2444	-0.8502	0.3762	0.5679	0.33	0.0073	0.4591	0.0583	0.7947	28.695	38.528	1.411
3	12.335	-6.4617	5.6928	14.7974	-0.7449	3.4563	0.1688	0.4269	-1.7127	-0.0077	0.1613	1.0465	0.3688	-0.015	-0.3301	0.7976	0.075	0.108	0.5929	-0.1305	1.0074	36.65	27.88	-1.187
4	3.286	-3.1148	1.6563	6.2517	4.2162	11.2233	0.6853	0.1195	-1.1021	0.1729	-0.3074	0.938	1.3992	-0.4812	-0.3779	0.6984	0.21	-0.2954	0.4509	-0.0157	0.9304	37.396	36.587	8.087
5	3.2162	3.8995	0.4496	14.7773	5.9538	3.1502	0.3892	0.4634	-0.4137	0.0485	-0.1495	-0.5531	0.1294	-0.0505	-0.2397	0.7384	0.466	-0.163	0.7654	-0.0165	0.7655	44.987	46.826	7.679
6	10.7321	4.3839	-5.8995	16.6665	-6.2006	13.1176	0.6648	0.9154	-0.0208	-1.0678	0.0478	-1.0942	-0.1463	0.8491	-0.7126	0.4677	0.2955	0.0948	0.8386	0.0246	0.8229	51.129	51.915	7.154
7	7.6719	-0.0194	1.9251	7.541	2.7931	5.8345	0.2813	0.6721	1.1543	-0.7063	0.1163	-1.264	-0.8517	1.1831	-0.3976	0.4221	0.0906	0.1874	0.5483	0.1402	0.753	50.8	61.874	10.046
8	9.7241	1.9722	3.8194	8.6016	4.667	6.2743	0.517	0.6267	-0.45	-0.8189	-0.4616	0.609	0.0713	-0.5246	-0.0553	0.4275	0.3008	-0.0767	0.6224	0.0655	0.6107	35.955	50.581	8.403
9	3.8816	-1.1549	1.4369	2.3915	0.712	4.3474	0.6439	-0.8826	-1.323	0.8008	-0.3958	0.5231	1.4226	-0.7549	-0.2481	0.9811	-0.1744	-0.138	0.7693	0.1675	0.872	36.606	41.556	17.786
10	9.0985	-0.637	-0.6622	13.2299	4.3149	14.3507	0.4559	-0.5069	-0.3667	0.9188	0.0985	-0.6734	0.767	0.3065	-0.5544	0.3574	0.2043	-0.0966	0.4752	0.1052	0.5567	47.333	50.246	19.059
11	2.5994	-1.4569	-2.4931	0.8449	1.6854	6.0719	0.3222	-0.0893	1.6003	-0.0896	0.4647	-0.8843	-1.0993	1.5173	-0.7869	0.5214	-0.1486	-0.1038	0.94	-0.0309	1.3338	56.555	62.921	18.571
12	7.8646	1.5227	1.4413	7.5115	2.8887	7.0293	0.3374	-1.1496	0.718	0.9655	0.01	-0.8461	-0.2067	0.4356	-0.3475	0.4358	0.1227	-0.0323	0.6237	-0.053	0.6797	46.31	59.888	24.171
13	14.0211	-3.489	1.5658	11.1832	4.3575	10.3307	0.5346	-0.4663	-0.2335	0.022	-0.7929	1.0669	0.5199	-1.256	0.2583	0.3701	0.1828	0.0663	0.7561	-0.0193	0.7294	31.051	55.67	18.019
14	3.2868	1.5799	2.4316	7.1968	-2.9051	7.177	0.2213	-0.24	0.3123	-0.884	-0.6819	1.5614	0.1447	-1.4764	0.4606	0.5964	0.4875	-0.2355	1.441	-0.3548	1.403	23.715	54.528	9.874
15	9.5263	1.2144	2.6328	6.273	2.7991	5.4282	0.1234	-0.0485	1.1785	-0.4976	-0.2874	0.1333	-0.9136	-0.4345	0.1639	0.55	0.2659	0.0479	0.5469	0.0552	0.8181	38.821	65.202	15.541

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	10 - 23
2	X-RAY DIFFRACTION	2	A	24 - 34
3	X-RAY DIFFRACTION	3	A	35 - 54
4	X-RAY DIFFRACTION	4	A	55 - 64
5	X-RAY DIFFRACTION	5	A	65 - 70
6	X-RAY DIFFRACTION	6	A	71 - 76
7	X-RAY DIFFRACTION	7	A	77 - 94
8	X-RAY DIFFRACTION	8	A	95 - 106
9	X-RAY DIFFRACTION	9	A	107 - 126
10	X-RAY DIFFRACTION	10	A	127 - 133
11	X-RAY DIFFRACTION	11	A	134 - 147
12	X-RAY DIFFRACTION	12	A	148 - 166
13	X-RAY DIFFRACTION	13	A	167 - 172
14	X-RAY DIFFRACTION	14	A	173 - 184
15	X-RAY DIFFRACTION	15	A	185 - 204

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