PDB-5efy: Apo-form of SCO3201

ID or keywords:

Entry

Database: PDB / ID: 5efy

Title

Apo-form of SCO3201

Components

Putative tetR-family transcriptional regulator

Keywords

TRANSCRIPTION / TetR-regulator / Apo-form / HTH-motif / bacterial transcription regulator

Function / homology

Function and homology information

transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function

Biological species

Streptomyces coelicolor (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Waack, P. / Hinrichs, W.

Citation

Journal: Febs J. / Year: 2022
Title: Crystal structures of free and ligand-bound forms of the TetR/AcrR-like regulator SCO3201 from Streptomyces coelicolor suggest a novel allosteric mechanism.
Authors: Werten, S. / Waack, P. / Palm, G.J. / Virolle, M.J. / Hinrichs, W.

History

Deposition	Oct 26, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Nov 16, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 14, 2022	Group: Database references / Category: citation / citation_author / database_2 Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5efy.cif.gz	285.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5efy.ent.gz	230.6 KB	Display	PDB format
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Validation report

Summary document	5efy_validation.pdf.gz	453.3 KB	Display	wwPDB validaton report
Full document	5efy_full_validation.pdf.gz	463.5 KB	Display
Data in XML	5efy_validation.xml.gz	27 KB	Display
Data in CIF	5efy_validation.cif.gz	36.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ef/5efy ftp://data.pdbj.org/pub/pdb/validation_reports/ef/5efy	HTTPS FTP

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Related structure data

Related structure data	7pt0C 4cgrS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5l90-1 4mf7-1 1vlp-4 4fbg-12 1vlp-2 4z8u-d 4ggp-1 4fbg-4 3pnx-1 5xuh-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative tetR-family transcriptional regulator

B: Putative tetR-family transcriptional regulator

C: Putative tetR-family transcriptional regulator

D: Putative tetR-family transcriptional regulator

93.3 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative tetR-family transcriptional regulator

B: Putative tetR-family transcriptional regulator

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

2

C: Putative tetR-family transcriptional regulator

D: Putative tetR-family transcriptional regulator

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

Unit cell

Length a, b, c (Å)	51.790, 98.426, 89.611
Angle α, β, γ (deg.)	90.00, 100.78, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ARG	ARG	THR	THR	A	A	28 - 117	8 - 97
2	1	ARG	ARG	THR	THR	B	B	28 - 117	8 - 97
1	2	THR	THR	LEU	LEU	A	A	26 - 116	6 - 96
2	2	THR	THR	LEU	LEU	C	C	26 - 116	6 - 96
1	3	GLU	GLU	THR	THR	A	A	32 - 115	12 - 95
2	3	GLU	GLU	THR	THR	D	D	32 - 115	12 - 95
1	4	SER	SER	SER	SER	A	A	126 - 203	106 - 183
2	4	SER	SER	SER	SER	B	B	126 - 203	106 - 183
1	5	SER	SER	SER	SER	A	A	126 - 203	106 - 183
2	5	SER	SER	SER	SER	C	C	126 - 203	106 - 183
1	6	TRP	TRP	SER	SER	A	A	127 - 203	107 - 183
2	6	TRP	TRP	SER	SER	D	D	127 - 203	107 - 183
1	7	PRO	PRO	ALA	ALA	A	A	212 - 227	192 - 207
2	7	PRO	PRO	ALA	ALA	B	B	212 - 227	192 - 207
1	8	PRO	PRO	PHE	PHE	A	A	212 - 226	192 - 206
2	8	PRO	PRO	PHE	PHE	C	C	212 - 226	192 - 206
1	9	GLU	GLU	ALA	ALA	A	A	214 - 227	194 - 207
2	9	GLU	GLU	ALA	ALA	D	D	214 - 227	194 - 207
1	10	ARG	ARG	LEU	LEU	B	B	28 - 116	8 - 96
2	10	ARG	ARG	LEU	LEU	C	C	28 - 116	8 - 96
1	11	GLU	GLU	THR	THR	B	B	32 - 115	12 - 95
2	11	GLU	GLU	THR	THR	D	D	32 - 115	12 - 95
1	12	SER	SER	SER	SER	B	B	123 - 204	103 - 184
2	12	SER	SER	SER	SER	C	C	123 - 204	103 - 184
1	13	TRP	TRP	SER	SER	B	B	127 - 203	107 - 183
2	13	TRP	TRP	SER	SER	D	D	127 - 203	107 - 183
1	14	ARG	ARG	PHE	PHE	B	B	210 - 226	190 - 206
2	14	ARG	ARG	PHE	PHE	C	C	210 - 226	190 - 206
1	15	GLU	GLU	ALA	ALA	B	B	214 - 227	194 - 207
2	15	GLU	GLU	ALA	ALA	D	D	214 - 227	194 - 207
1	16	GLU	GLU	THR	THR	C	C	32 - 115	12 - 95
2	16	GLU	GLU	THR	THR	D	D	32 - 115	12 - 95
1	17	TRP	TRP	SER	SER	C	C	127 - 203	107 - 183
2	17	TRP	TRP	SER	SER	D	D	127 - 203	107 - 183
1	18	GLU	GLU	PHE	PHE	C	C	214 - 226	194 - 206
2	18	GLU	GLU	PHE	PHE	D	D	214 - 226	194 - 206

NCS ensembles :

#1: Protein	Putative tetR-family transcriptional regulator Mass: 23313.471 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SCO3201 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KYU4
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.22 Å³/Da / Density % sol: 44.7 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 12 % Ethanol; 0.1 M Tris/HCl; pH 5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 11, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.918 Å / Relative weight: 1
Reflection	Resolution: 2.7→94.6 Å / Num. obs: 23495 / % possible obs: 96.6 % / Redundancy: 3 % / Net I/σ(I): 7.7
Reflection shell	Resolution: 2.7→2.85 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.5 / Mean I/σ(I) obs: 1.44

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4cgr

4cgr

Resolution: 2.7→88.03 Å / Cor.coef. F_o:F_c: 0.921 / Cor.coef. F_o:F_c free: 0.862 / SU B: 38.759 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R: 1.742 / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29733	1227	5.2 %	RANDOM
R_work	0.25833	-	-	-
obs	0.26037	22236	96.65 %	-

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: 77.619 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.29 Å²	-0 Å²	-5.64 Å²
2-	-	3.54 Å²	0 Å²
3-	-	-	0.83 Å²

Refinement step

Cycle: 1 / Resolution: 2.7→88.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5309	0	0	23	5332

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	5410
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	5145
X-RAY DIFFRACTION	r_angle_refined_deg	1.443	1.945	7401
X-RAY DIFFRACTION	r_angle_other_deg	1.347	3.001	11534
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.679	5	747
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.319	21.364	176
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.46	15	693
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.539	15	47
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	885
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	6269
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	1210
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	2.565	3.988	3021
X-RAY DIFFRACTION	r_mcbond_other	2.566	3.988	3020
X-RAY DIFFRACTION	r_mcangle_it	4.084	5.969	3757
X-RAY DIFFRACTION	r_mcangle_other	4.083	5.969	3758
X-RAY DIFFRACTION	r_scbond_it	2.603	4.143	2389
X-RAY DIFFRACTION	r_scbond_other	2.603	4.142	2390
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.206	6.142	3644
X-RAY DIFFRACTION	r_long_range_B_refined	8.283	37.927	23541
X-RAY DIFFRACTION	r_long_range_B_other	8.285	37.925	23539
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	3990	0.14
1	2	B	3990	0.14
2	1	A	3865	0.14
2	2	C	3865	0.14
3	1	A	3329	0.13
3	2	D	3329	0.13
4	1	A	3362	0.13
4	2	B	3362	0.13
5	1	A	3146	0.16
5	2	C	3146	0.16
6	1	A	2861	0.15
6	2	D	2861	0.15
7	1	A	622	0.18
7	2	B	622	0.18
8	1	A	575	0.2
8	2	C	575	0.2
9	1	A	431	0.27
9	2	D	431	0.27
10	1	B	4293	0.12
10	2	C	4293	0.12
11	1	B	3563	0.15
11	2	D	3563	0.15
12	1	B	3291	0.16
12	2	C	3291	0.16
13	1	B	2866	0.14
13	2	D	2866	0.14
14	1	B	665	0.22
14	2	C	665	0.22
15	1	B	427	0.29
15	2	D	427	0.29
16	1	C	3457	0.14
16	2	D	3457	0.14
17	1	C	2735	0.15
17	2	D	2735	0.15
18	1	C	411	0.28
18	2	D	411	0.28

LS refinement shell

Resolution: 2.703→2.773 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.492	85	-
R_work	0.404	1581	-
obs	-	-	94.44 %

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	4.112	-0.5163	0.1625	6.3696	3.0589	3.6539	0.2027	0.3427	-0.1265	0.3644	-0.3305	0.1828	0.3703	-0.6042	0.1278	0.3113	0.0379	0.2081	0.3431	0.0173	0.162	-22.4116	8.7773	42.5365
2	3.2774	0.4043	0.4585	3.187	2.291	9.3283	0.057	0.2645	-0.0081	0.0794	-0.011	-0.3413	-0.3375	0.5241	-0.0459	0.1634	0.0135	0.0966	0.0702	0.0474	0.136	-2.2938	16.2556	39.2066
3	3.111	-1.0359	0.3205	1.5808	-1.9417	7.0809	-0.0447	-0.2147	-0.2176	0.221	0.1457	-0.1074	-0.0104	0.2702	-0.101	0.3512	0.0056	0.11	0.3142	-0.0698	0.1585	-17.9921	20.5988	-4.382
4	6.2002	-3.5675	3.8286	6.1043	-3.2475	3.1322	-0.6776	-1.0654	0.0588	0.3715	0.9112	0.1649	-0.2928	-0.5097	-0.2336	0.4598	0.1082	0.1791	0.547	-0.0517	0.2921	-36.3074	32.7243	1.6151

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	26 - 228
2	X-RAY DIFFRACTION	2	B	28 - 228
3	X-RAY DIFFRACTION	3	C	26 - 227
4	X-RAY DIFFRACTION	4	D	32 - 228

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