PDB-3dew: The structure of a putative TetR family transcriptional regulator...

ID or keywords:

Entry

Database: PDB / ID: 3dew

Title

The structure of a putative TetR family transcriptional regulator from Geobacter sulfurreducens PCA.

Components

Transcriptional regulator, TetR family

Keywords

transcription regulator / TetR / transcriptional regulator / Geobacter sulfurreducens / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding / Transcription / Transcription regulation

Function / homology

Function and homology information

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

Biological species

Geobacter sulfurreducens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.75 Å

Authors

Cuff, M.E. / Bigelow, L. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: The structure of a putative TetR family transcriptional regulator from Geobacter sulfurreducens PCA.
Authors: Cuff, M.E. / Bigelow, L. / Abdullah, J. / Joachimiak, A.

History

Deposition	Jun 10, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 30, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3dew.cif.gz	57.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3dew.ent.gz	45.3 KB	Display	PDB format
PDBx/mmJSON format	3dew.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3dew_validation.pdf.gz	451.2 KB	Display	wwPDB validaton report
Full document	3dew_full_validation.pdf.gz	452.2 KB	Display
Data in XML	3dew_validation.xml.gz	11.4 KB	Display
Data in CIF	3dew_validation.cif.gz	16.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/de/3dew ftp://data.pdbj.org/pub/pdb/validation_reports/de/3dew	HTTPS FTP

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Related structure data

Similar structure data	3zm9-1 5fut-d 4cga-d 4cg8-d 4w4v-d 3zm9-2 4cg9-d 3lq3-d 2i7q-d 1dnl-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: apc88507

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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) #234 - Jun 2019 MDM2 and Cancer similarity (1) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (1) #9 - Sep 2000 Lysozyme similarity (1)

Deposited unit

A: Transcriptional regulator, TetR family

hetero molecules

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

1

A: Transcriptional regulator, TetR family

hetero molecules

A: Transcriptional regulator, TetR family

hetero molecules

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

Unit cell

Length a, b, c (Å)	63.106, 63.106, 76.550
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	A-276- HOH

Details

authors state that the biological assembly is likely dimer

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Protein , 1 types, 1 molecules A

#1: Protein	Transcriptional regulator, TetR family Mass: 22780.838 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: PCA / Gene: GSU0175 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q74GS0

#1: Protein

Transcriptional regulator, TetR family

Mass: 22780.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Geobacter sulfurreducens (bacteria) / Strain: PCA / Gene: GSU0175 / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q74GS0

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Non-polymers , 5 types, 168 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-BME / BETA-MERCAPTOETHANOL Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₄O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 162 / 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: 1.93 Å³/Da / Density % sol: 36.32 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M Na Acetate pH4.6, 4% PEG 4K, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97915,0.97937

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2007

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	0.97915	1
2	0.97937	1

Reflection

Resolution: 1.75→44.5 Å / Num. obs: 18099 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / B_iso Wilson estimate: 24.6 Å² / R_merge(I) obs: 0.074 / R_sym value: 0.074 / Net I/σ(I): 9.8

Reflection shell

Resolution: 1.75→1.79 Å / Redundancy: 10.8 % / R_merge(I) obs: 0.483 / % possible all: 100

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 1.75 Å / D res low: 50 Å / FOM : 0.462 / FOM acentric: 0.483 / FOM centric: 0.298 / Reflection: 18099 / Reflection acentric: 16078 / Reflection centric: 2021

Phasing MAD set

Highest resolution: 1.75 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	1.72	1	0.1	0.1	0	0	16078	2021
2	0.88	0.8	5.7	8.3	0.8	0.66	12542	1704

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	11.25-50	1.5	1	0.6	0.4	0	0	42	37
1	6.34-11.25	1.48	1	0.6	0.4	0	0	237	92
1	4.41-6.34	1.32	1	0.4	0.3	0	0	636	154
1	3.38-4.41	1.07	1	0.3	0.3	0	0	1195	216
1	2.74-3.38	1.55	1	0.2	0.1	0	0	1926	274
1	2.31-2.74	1.85	1	0.1	0.1	0	0	2864	349
1	1.99-2.31	3.57	1	0.1	0	0	0	3971	423
1	1.75-1.99	9.87	1	0	0	0	0	5207	476
2	11.25-50	0.57	0.82	12.2	18.7	2.07	0.92	42	37
2	6.34-11.25	0.62	0.56	8.6	13.4	2.01	1.36	237	92
2	4.41-6.34	0.7	0.63	7.3	8.4	1.72	1.24	636	154
2	3.38-4.41	0.82	0.72	7.4	9.3	1.16	0.85	1195	215
2	2.74-3.38	0.86	0.85	6.1	7.9	0.97	0.68	1926	274
2	2.31-2.74	0.9	0.87	4.7	6.8	0.8	0.48	2864	349
2	1.99-2.31	0.97	0.96	5.2	7.4	0.45	0.3	3953	421
2	1.75-1.99	0.99	1	5.9	8.1	0.28	0.18	1689	162

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	36.27165	-0.187	-0.05	-0.157	0
2	Se	20.27432	-0.251	0.043	-0.323	0
3	Se	27.79353	-0.158	0.166	-0.412	0
4	Se	98.9109	-0.229	0.167	0.036	0
5	Se	27.78613	-0.029	0.055	-0.351	0
6	Se	120.85499	-0.45	-0.095	0.038	0
7	Se	25.18532	-0.123	0.161	-0.393	0
8	Se	43.06	-0.482	-0.101	0.01	0
9	Se	39.1768	-0.191	-0.054	-0.157	-0.129
10	Se	20.98783	-0.251	0.044	-0.323	-0.123
11	Se	27.89173	-0.158	0.166	-0.412	-0.106
12	Se	122.24792	-0.227	0.168	0.035	-0.167
13	Se	23.47188	-0.027	0.056	-0.351	-0.069
14	Se	136.77164	-0.442	-0.097	0.039	-0.159
15	Se	22.45054	-0.124	0.16	-0.393	-0.042
16	Se	36.58893	-0.482	-0.1	0.008	-0.049

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
11.25-50	0.695	0.898	0.463	79	42	37
6.34-11.25	0.804	0.857	0.669	329	237	92
4.41-6.34	0.8	0.85	0.597	790	636	154
3.38-4.41	0.728	0.77	0.492	1411	1195	216
2.74-3.38	0.694	0.733	0.418	2200	1926	274
2.31-2.74	0.625	0.66	0.338	3213	2864	349
1.99-2.31	0.423	0.448	0.183	4394	3971	423
1.75-1.99	0.175	0.189	0.031	5683	5207	476

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 18099

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
5.93-100	42.1	0.879	501
4.68-5.93	33.9	0.933	505
4.07-4.68	39.9	0.919	507
3.68-4.07	39.4	0.933	509
3.41-3.68	42.9	0.917	513
3.2-3.41	43.2	0.895	505
3.04-3.2	40.3	0.919	525
2.89-3.04	44.7	0.909	551
2.77-2.89	42	0.919	579
2.66-2.77	38	0.919	606
2.56-2.66	41	0.92	620
2.47-2.56	43	0.917	651
2.39-2.47	46	0.897	663
2.32-2.39	43.8	0.914	687
2.25-2.32	47.5	0.901	700
2.19-2.25	50.5	0.892	725
2.13-2.19	54.6	0.89	763
2.08-2.13	57.1	0.898	762
2.03-2.08	58.6	0.872	760
1.99-2.03	58.7	0.868	806
1.95-1.99	67.5	0.876	822
1.91-1.95	65.6	0.862	814
1.87-1.91	74.1	0.811	854
1.83-1.87	80.6	0.846	867
1.8-1.83	78.3	0.818	868
1.75-1.8	78.9	0.808	1436

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	5	phasing
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
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: 1.75→44.5 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.949 / SU B: 4.961 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.123
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21	926	5.1 %	RANDOM
R_work	0.171	-	-	-
all	0.173	18099	-	-
obs	0.173	18099	99.3 %	-

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: 17.335 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.43 Å²	0.22 Å²	0 Å²
2-	-	0.43 Å²	0 Å²
3-	-	-	-0.65 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→44.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1477	0	21	162	1660

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	1725
X-RAY DIFFRACTION	r_angle_refined_deg	1.43	1.961	2351
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.846	5	233
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.301	22.692	78
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.456	15	289
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	25.063	15	17
X-RAY DIFFRACTION	r_chiral_restr	0.101	0.2	255
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1368
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	862
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	1265
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.141	0.2	146
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.232	0.2	103
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.143	0.2	22
X-RAY DIFFRACTION	r_mcbond_it	1.277	1.5	1115
X-RAY DIFFRACTION	r_mcangle_it	1.538	2	1753
X-RAY DIFFRACTION	r_scbond_it	2.92	3	686
X-RAY DIFFRACTION	r_scangle_it	4.285	4.5	598

LS refinement shell

Resolution: 1.751→1.797 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.269	69	-
R_work	0.19	1249	-
all	-	1318	-
obs	-	-	99.4 %

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	5.295	2.5276	0.6813	1.9158	-0.7717	6.2632	0.5272	-0.7146	-0.4389	0.311	-0.361	-0.4724	-0.0642	0.4294	-0.1662	0.137	-0.1097	-0.0817	0.1654	0.0754	0.1472	-23.9856	39.3277	-1.4577
2	1.7087	4.9389	0.0196	14.3322	0.2801	0.8847	-0.0157	0.1035	-0.2748	0.0712	-0.1788	-1.0581	0.195	0.2731	0.1945	0.0011	-0.0005	-0.0174	0.0965	0.0588	0.1581	-32.0346	22.0731	-7.0941
3	2.2132	1.69	2.7058	5.1297	3.8077	5.8027	-0.1761	-0.0148	0.0025	0.0649	0.0154	-0.1497	0.3296	0.2234	0.1607	0.1523	0.0407	0.0489	0.0545	0.0051	0.0382	-40.5797	11.1011	-0.7972
4	0.9454	1.1984	0.1553	5.0594	0.6372	0.9899	-0.0114	0.0781	-0.0676	0.1522	-0.1435	-0.0691	0.1564	0.0463	0.1548	0.0543	-0.0095	0.0241	0.0884	-0.0099	0.0381	-44.2891	19.5183	-9.1245
5	1.2227	0.6232	0.9661	4.7022	5.1046	8.883	-0.0596	0.0866	-0.1175	0.163	-0.159	0.1772	0.3319	-0.3284	0.2186	0.1156	-0.0328	0.0529	0.0829	-0.0098	0.1035	-51.1259	17.4668	-1.6285
6	2.7122	-0.2533	-0.5877	0.9877	1.7393	4.5024	-0.2384	-0.0947	-0.3294	0.3405	0.0637	-0.0069	0.6114	0.2128	0.1747	0.2498	0.0323	0.0884	0.0284	0.0436	0.0925	-49.5419	11.085	8.781

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 49
2	X-RAY DIFFRACTION	2	A	50 - 72
3	X-RAY DIFFRACTION	3	A	73 - 96
4	X-RAY DIFFRACTION	4	A	97 - 142
5	X-RAY DIFFRACTION	5	A	143 - 168
6	X-RAY DIFFRACTION	6	A	169 - 196

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