PDB-3bqy: Crystal structure of a possible TetR family transcriptional regul...

ID or keywords:

Entry

Database: PDB / ID: 3bqy

Title

Crystal structure of a possible TetR family transcriptional regulator from Streptomyces coelicolor A3(2).

Components

Putative TetR family transcriptional regulator

Keywords

TRANSCRIPTION REGULATOR / TetR / transcriptional regulator / structural genomics / Streptomyces coelicolor / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding / Transcription regulation

Function / homology

Function and homology information

transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / metal ion binding
Similarity search - Function

Biological species

Streptomyces coelicolor A3

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.95 Å

Authors

Cuff, M.E. / Skarina, T. / Kagan, O. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: Structure of a possible TetR family transcriptional regulator from Streptomyces coelicolor A3(2).
Authors: Cuff, M.E. / Skarina, T. / Kagan, O. / Edwards, A.M. / Savchenko, A. / Joachimiak, A.

History

Deposition	Dec 20, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 15, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3bqy.cif.gz	55.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3bqy.ent.gz	41.8 KB	Display	PDB format
PDBx/mmJSON format	3bqy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3bqy_validation.pdf.gz	445.5 KB	Display	wwPDB validaton report
Full document	3bqy_full_validation.pdf.gz	446.7 KB	Display
Data in XML	3bqy_validation.xml.gz	11.5 KB	Display
Data in CIF	3bqy_validation.cif.gz	16.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bq/3bqy ftp://data.pdbj.org/pub/pdb/validation_reports/bq/3bqy	HTTPS FTP

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Related structure data

Similar structure data	2zcx-1 6gdr-d 1gmo-4 6rxb-1 2ns8-2 3zqh-1 3r2n-d 4d5c-1 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: APC6288

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: Putative TetR family transcriptional regulator

hetero molecules

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

1

A: Putative TetR family transcriptional regulator

hetero molecules

A: Putative TetR family transcriptional regulator

hetero molecules

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

Unit cell

Length a, b, c (Å)	83.755, 83.755, 83.700
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Putative TetR family transcriptional regulator Mass: 22113.133 Da / Num. of mol.: 1 / Fragment: Residues 16-220 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria) Species: Streptomyces coelicolor / Strain: A3(2) / M145 / Gene: SCO0250, SCJ9A.29 / Plasmid: modified p11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9S1P1
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₄O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 181 / 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: 3.32 Å³/Da / Density % sol: 62.94 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% PEG 3350, 0.1M HEPES pH 7.5, 20% Sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.97932, 0.97948

Detector

Type: CUSTOM-MADE / Detector: CCD / Date: Dec 18, 2006

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97932	1
2	0.97948	1

Reflection

Redundancy: 8.1 % / Av σ(I) over netI: 7.9 / Number: 195817 / R_merge(I) obs: 0.103 / Χ²: 2.02 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 24079 / % possible obs: 99.8

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.68	50	98.9	1	0.082	7.432	7.6
3.72	4.68	99.5	1	0.072	4.375	6.7
3.25	3.72	100	1	0.075	3.395	7.7
2.95	3.25	100	1	0.095	2.64	8
2.74	2.95	100	1	0.106	2.095	8.1
2.58	2.74	100	1	0.119	1.681	8.2
2.45	2.58	100	1	0.134	1.417	8.3
2.34	2.45	100	1	0.145	1.246	8.4
2.25	2.34	100	1	0.172	1.1	8.4
2.17	2.25	100	1	0.192	1.027	8.4
2.11	2.17	100	1	0.237	0.985	8.5
2.05	2.11	99.8	1	0.314	0.942	8.5
1.99	2.05	99.9	1	0.404	0.843	8.5
1.94	1.99	99.7	1	0.539	0.861	8.5
1.9	1.94	99.6	1	0.692	0.84	8.4

Reflection

Resolution: 1.94→50 Å / Num. all: 24079 / Num. obs: 24079 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / B_iso Wilson estimate: 27.8 Å² / R_merge(I) obs: 0.103 / Χ²: 2.017 / Net I/σ(I): 7.9

Reflection shell

Resolution: 1.94→1.99 Å / Redundancy: 8.4 % / R_merge(I) obs: 0.539 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1583 / Χ²: 0.84 / % possible all: 99.7

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 1.95 Å / D res low: 50 Å / FOM : 0.462 / FOM acentric: 0.482 / FOM centric: 0.341 / Reflection: 22231 / Reflection acentric: 19132 / Reflection centric: 3099

Phasing MAD set

Highest resolution: 1.95 Å / Lowest resolution: 50 Å

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	1.99	1	0.3	0.2	0	0	19132	3099
2	0.88	0.81	7.6	11	0.9	0.74	19119	3092

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	12.25-50	1.37	1	0.9	0.5	0	0	49	59
1	6.98-12.25	1.48	1	0.9	0.5	0	0	279	153
1	4.88-6.98	2.32	1	0.9	0.4	0	0	751	263
1	3.75-4.88	1.24	1	0.6	0.4	0	0	1414	337
1	3.05-3.75	1.62	1	0.5	0.3	0	0	2289	440
1	2.57-3.05	2.37	1	0.4	0.1	0	0	3396	526
1	2.22-2.57	2.49	1	0.3	0.1	0	0	4736	624
1	1.95-2.22	2.87	1	0.2	0.1	0	0	6218	697
2	12.25-50	0.77	0.9	12.6	17.3	1.7	1.34	49	57
2	6.98-12.25	0.75	0.68	11.8	15.7	1.7	1.3	278	153
2	4.88-6.98	0.62	0.62	9.3	12.4	1.97	1.27	751	263
2	3.75-4.88	0.78	0.74	10.1	14.1	1.33	0.84	1414	337
2	3.05-3.75	0.79	0.74	8.3	11.4	1.26	0.9	2288	440
2	2.57-3.05	0.86	0.85	7	9.4	1.03	0.7	3396	525
2	2.22-2.57	0.95	0.93	7	9.4	0.72	0.49	4734	622
2	1.95-2.22	1	0.99	7.3	9.9	0.45	0.28	6209	695

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	32.24762	-0.361	-0.17	-0.081	0
2	Se	40.58062	-0.402	-0.251	-0.112	0
3	Se	40.14969	-0.481	-0.182	-0.109	0
4	Se	55.55269	-0.304	-0.105	-0.057	0
5	Se	28.28687	-0.361	-0.17	-0.081	-0.197
6	Se	37.58278	-0.402	-0.251	-0.112	-0.153
7	Se	42.56535	-0.481	-0.183	-0.109	-0.131
8	Se	52.60303	-0.304	-0.105	-0.057	-0.089

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
12.25-50	0.601	0.737	0.489	108	49	59
6.98-12.25	0.68	0.729	0.591	432	279	153
4.88-6.98	0.756	0.821	0.571	1014	751	263
3.75-4.88	0.669	0.716	0.473	1751	1414	337
3.05-3.75	0.663	0.698	0.483	2729	2289	440
2.57-3.05	0.571	0.603	0.36	3922	3396	526
2.22-2.57	0.421	0.445	0.235	5360	4736	624
1.95-2.22	0.242	0.256	0.113	6915	6218	697

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 23996

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.23-100	42.6	0.877	504
5.65-7.23	33.5	0.937	509
4.9-5.65	37	0.935	512
4.43-4.9	37.5	0.938	524
4.07-4.43	43.5	0.932	556
3.78-4.07	39.9	0.94	625
3.55-3.78	38.6	0.932	645
3.36-3.55	37.8	0.928	690
3.19-3.36	39.1	0.92	705
3.05-3.19	45.5	0.894	764
2.92-3.05	40.8	0.91	783
2.81-2.92	44	0.914	822
2.71-2.81	40.9	0.913	833
2.62-2.71	43.9	0.914	875
2.54-2.62	43.9	0.92	890
2.47-2.54	45.7	0.912	908
2.4-2.47	50.1	0.916	961
2.34-2.4	50.8	0.914	967
2.28-2.34	53.4	0.916	1003
2.23-2.28	53.6	0.918	1023
2.18-2.23	55.3	0.913	1065
2.13-2.18	57.7	0.918	1060
2.08-2.13	62.5	0.914	1095
2.04-2.08	61.8	0.912	1068
2-2.04	67.7	0.903	1166
1.97-2	70.7	0.88	1151
1.93-1.97	81.6	0.835	1149
1.9-1.93	87.9	0.692	1143

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	5	phasing
REFMAC		refinement
PDB_EXTRACT	3.004	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building

Refinement

Method to determine structure:

MAD / Resolution: 1.95→34.18 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.946 / SU B: 5.514 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.121
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21	1129	5.1 %	RANDOM
R_work	0.181	-	-	-
all	0.183	22229	-	-
obs	0.183	22229	99.77 %	-

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: 31.652 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.54 Å²	0 Å²	0 Å²
2-	-	0.54 Å²	0 Å²
3-	-	-	-1.09 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→34.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1518	0	14	181	1713

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.021	1621
X-RAY DIFFRACTION	r_angle_refined_deg	1.28	1.964	2210
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.378	5	220
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.441	21.667	78
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.844	15	249
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.153	15	23
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	251
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1269
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	769
X-RAY DIFFRACTION	r_nbtor_refined	0.301	0.2	1130
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	149
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.218	0.2	101
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.193	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	0.936	1.5	1062
X-RAY DIFFRACTION	r_mcangle_it	1.48	2	1633
X-RAY DIFFRACTION	r_scbond_it	2.285	3	612
X-RAY DIFFRACTION	r_scangle_it	3.362	4.5	570

LS refinement shell

Resolution: 1.95→2.001 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.295	81	-
R_work	0.228	1498	-
all	-	1579	-
obs	-	-	99.43 %

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	4.4229	-2.6085	-1.5001	6.4675	4.1096	10.2435	-0.0806	-0.0455	-0.1824	-0.2532	-0.4965	1.1481	-0.7053	-0.6148	0.5772	-0.0373	0.0447	-0.0852	-0.0689	-0.0101	0.1431	6.4653	59.0063	28.7214
2	1.4669	-0.5309	0.4881	0.9156	-0.6487	2.0002	0.0697	0.0481	0.0063	0.0172	0.0743	0.1523	0.012	-0.0034	-0.1441	-0.0429	-0.0193	0.0162	-0.1062	0.0253	-0.0747	27.026	44.3865	28.5747
3	0.3041	-0.5911	-0.7067	1.6075	0.4171	3.637	0.1331	0.2688	0.1648	-0.3651	0.0472	0.1985	-0.012	-0.7654	-0.1803	-0.0161	-0.0116	-0.0612	0.23	0.0799	0.0168	30.4766	51.9318	2.2111
4	9.153	-1.5897	5.3446	1.8454	-0.7265	6.0543	0.1128	-0.0175	-0.079	-0.065	0.0141	0.0395	0.4244	-0.027	-0.1269	-0.0018	0.0019	0.0265	-0.0596	0.0093	-0.1213	36.1875	39.7285	19.6525

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	16 - 66	3 - 53
2	X-RAY DIFFRACTION	2	A	A	67 - 163	54 - 150
3	X-RAY DIFFRACTION	3	A	A	164 - 200	151 - 187
4	X-RAY DIFFRACTION	4	A	A	201 - 220	188 - 207

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