PDB-3jw4: The structure of a putative MarR family transcriptional regulator...

ID or keywords:

Entry

Database: PDB / ID: 3jw4

Title

The structure of a putative MarR family transcriptional regulator from Clostridium acetobutylicum

Components

Transcriptional regulator, MarR/EmrR family

Transcriptional regulation

Keywords

Transcription regulator / MarR / emrR /

transcriptional regulator /

DNA-binding protein /

Structural Genomics / PSI-2 /

Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding /

Transcription /

Transcription regulation

Function / homology

Function and homology information

DNA-binding transcription factor activity
Similarity search - Function

Biological species

Clostridium acetobutylicum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.1 Å

Authors

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

Citation

Journal: TO BE PUBLISHED
Title: The structure of a putative MarR family transcriptional regulator from Clostridium acetobutylicum
Authors: Cuff, M.E. / Bigelow, L. / Moy, S. / Joachimiak, A.

History

Deposition	Sep 17, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 22, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3jw4.cif.gz	95.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3jw4.ent.gz	77 KB	Display	PDB format
PDBx/mmJSON format	3jw4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jw/3jw4 ftp://data.pdbj.org/pub/pdb/validation_reports/jw/3jw4	HTTPS FTP

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Related structure data

Similar structure data	3eco-d 3f22-d 2hyf-1 5ffx-1 6fi9-1 5yhx-2 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
Other databases	TargetDB: APC89001

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: Transcriptional regulator, MarR/EmrR family

B: Transcriptional regulator, MarR/EmrR family

C: Transcriptional regulator, MarR/EmrR family

hetero molecules

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

1

A: Transcriptional regulator, MarR/EmrR family

B: Transcriptional regulator, MarR/EmrR family

hetero molecules

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

2

C: Transcriptional regulator, MarR/EmrR family

hetero molecules

C: Transcriptional regulator, MarR/EmrR family

hetero molecules

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

Unit cell

Length a, b, c (Å)	105.115, 53.295, 90.821
Angle α, β, γ (deg.)	90.000, 112.020, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	C-261- HOH

#1: Protein	Transcriptional regulator, MarR/EmrR family / Transcriptional regulation Mass: 17155.631 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Strain: ATCC 824 / Gene: CAC2486, CA_C2486 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): modified BL21 / References: UniProt: Q97G83
#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-IMD / IMIDAZOLE / Imidazole Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₅N₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.29 Å³/Da / Density % sol: 46.31 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M potassium thiocyanate, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.97949, 0.97935

Detector

Type: CUSTOM-MADE / Detector: CCD / Date: Mar 5, 2008

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	0.97949	1
2	0.97935	1

Reflection

Redundancy: 7.6 % / Number: 210625 / R_merge(I) obs: 0.092 / Χ²: 1.79 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 27599 / % possible obs: 99.6

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.7	50	95.9	1	0.085	9.742	7.4
4.52	5.7	98.8	1	0.068	4.794	6.2
3.95	4.52	98.8	1	0.059	3.145	7.3
3.59	3.95	99.6	1	0.065	2.589	7.5
3.33	3.59	100	1	0.072	2.161	7.6
3.14	3.33	100	1	0.079	1.692	7.7
2.98	3.14	100	1	0.096	1.414	7.8
2.85	2.98	100	1	0.109	1.278	7.8
2.74	2.85	100	1	0.126	1.111	7.8
2.65	2.74	100	1	0.14	1.029	7.9
2.56	2.65	100	1	0.158	0.926	7.9
2.49	2.56	100	1	0.179	0.857	7.9
2.42	2.49	100	1	0.208	0.889	7.9
2.37	2.42	100	1	0.239	0.86	8
2.31	2.37	100	1	0.241	0.798	7.9
2.26	2.31	100	1	0.284	0.754	7.9
2.22	2.26	100	1	0.32	0.735	7.9
2.18	2.22	99.9	1	0.334	0.76	7.8
2.14	2.18	99.9	1	0.39	0.722	7.4
2.1	2.14	99.8	1	0.453	0.673	7

Reflection

Resolution: 2.1→50 Å / Num. all: 27599 / Num. obs: 27599 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / B_iso Wilson estimate: 31.2 Å² / R_merge(I) obs: 0.092 / Net I/σ(I): 7.8

Reflection shell

Resolution: 2.1→2.14 Å / Redundancy: 7 % / R_merge(I) obs: 0.453 / % possible all: 99.8

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2.1 Å / D res low: 50 Å / FOM : 0.343 / FOM acentric: 0.349 / FOM centric: 0.26 / Reflection: 27301 / Reflection acentric: 25773 / Reflection centric: 1528

Phasing MAD set

Highest resolution: 2.1 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	1.69	1	0.2	0.1	0	0	25773	1528
2	0.93	0.87	11.9	17.5	0.55	0.48	23079	1404

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	12.98-50	1.42	1	0.9	0.5	0	0	74	29
1	7.46-12.98	1.31	1	0.9	0.6	0	0	412	76
1	5.23-7.46	1.91	1	0.6	0.3	0	0	1067	127
1	4.03-5.23	1.15	1	0.4	0.4	0	0	1953	161
1	3.28-4.03	1.22	1	0.2	0.2	0	0	3119	211
1	2.76-3.28	2.89	1	0.1	0	0	0	4597	265
1	2.39-2.76	5.95	1	0.1	0	0	0	6268	309
1	2.1-2.39	1.7	1	0.1	0	0	0	8283	350
2	12.98-50	0.8	0.64	18.4	21.9	1.97	1.36	70	29
2	7.46-12.98	0.78	0.81	16.8	20.6	1.73	1.18	408	76
2	5.23-7.46	0.77	0.7	14.2	16.5	1.49	1.22	1060	127
2	4.03-5.23	0.89	0.78	17.4	23	0.85	0.61	1942	154
2	3.28-4.03	0.92	0.88	14.8	19.5	0.65	0.43	3115	205
2	2.76-3.28	0.95	0.92	11	16.7	0.52	0.32	4581	262
2	2.39-2.76	0.98	0.98	9.8	14.4	0.32	0.2	6242	307
2	2.1-2.39	1	0.99	10.7	16.1	0.17	0.1	5661	244

Phasing MAD set site

Atom type symbol: Se

ID	B iso	Fract x	Fract y	Fract z	Occupancy	Occupancy iso
1	44.3369	-0.245	-0.064	-0.291	3.803	0
2	46.5264	-0.072	-0.156	-0.239	3.6	0
3	54.1299	-0.351	0.014	-0.227	3.943	0
4	56.6506	-0.51	-0.136	-0.106	3.8	0
5	64.639	-0.362	-0.215	-0.387	3.113	0
6	45.8579	-0.404	-0.276	0.028	2.832	0
7	43.6785	-0.425	0.043	-0.409	2.966	0
8	59.5855	-0.215	-0.139	-0.18	2.183	0
9	141.0039	-0.068	-0.171	-0.196	3.96	0
10	64.6119	-0.597	-0.216	-0.327	2.985	0
11	63.8004	-0.568	-0.228	-0.289	2.632	0
12	107.3945	0.148	-0.073	-0.153	2.01	0
13	26.225	-0.187	-0.358	-0.326	0.17	0
14	206.9072	-0.443	-0.244	-0.323	3.909	0
15	44.46	-0.292	0.228	-0.338	0.253	0
16	46.4231	0.185	-0.082	-0.124	1.818	0
17	43.114	-0.245	-0.064	-0.291	3.764	-0.14
18	46.7796	-0.072	-0.155	-0.238	3.196	-0.153
19	56.5209	-0.351	0.014	-0.227	3.449	-0.144
20	57.4155	-0.51	-0.136	-0.106	3.33	-0.153
21	58.941	-0.363	-0.214	-0.387	2.616	-0.126
22	44.6205	-0.405	-0.275	0.027	2.205	-0.093
23	44.3968	-0.425	0.044	-0.408	2.46	-0.114
24	53.1269	-0.215	-0.14	-0.179	1.881	-0.086
25	137.2569	-0.068	-0.171	-0.196	3.557	-0.13
26	72.1076	-0.597	-0.216	-0.327	2.853	-0.114
27	67.4419	-0.569	-0.229	-0.289	2.221	-0.103
28	127.0824	0.149	-0.072	-0.153	2.01	-0.06
29	27.936	-0.186	-0.356	-0.328	0.155	-0.018
30	192.8295	-0.441	-0.242	-0.321	3.164	-0.084
31	122.502	-0.293	0.237	-0.348	0.486	-0.012
32	47.7326	0.184	-0.08	-0.124	1.48	-0.049

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
12.98-50	0.674	0.726	0.54	103	74	29
7.46-12.98	0.744	0.776	0.575	488	412	76
5.23-7.46	0.755	0.774	0.598	1194	1067	127
4.03-5.23	0.642	0.658	0.457	2114	1953	161
3.28-4.03	0.573	0.591	0.314	3330	3119	211
2.76-3.28	0.443	0.454	0.259	4862	4597	265
2.39-2.76	0.257	0.263	0.127	6577	6268	309
2.1-2.39	0.108	0.111	0.04	8633	8283	350

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 27301

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.88-100	55.8	0.851	506
6.3-7.88	54.1	0.87	520
5.49-6.3	51.5	0.856	514
4.95-5.49	55.5	0.838	567
4.54-4.95	52.8	0.883	615
4.21-4.54	51	0.896	687
3.95-4.21	47.5	0.877	720
3.73-3.95	51	0.863	777
3.55-3.73	53.5	0.858	805
3.39-3.55	56.1	0.843	856
3.25-3.39	57.8	0.833	891
3.12-3.25	56.6	0.834	902
3.01-3.12	57.5	0.815	974
2.91-3.01	58.7	0.796	987
2.82-2.91	59	0.79	1015
2.74-2.82	63.8	0.776	1058
2.66-2.74	64.8	0.801	1069
2.59-2.66	63.6	0.792	1131
2.53-2.59	65.6	0.802	1146
2.47-2.53	64.6	0.807	1149
2.41-2.47	66.7	0.794	1215
2.36-2.41	69.1	0.804	1209
2.31-2.36	69.5	0.818	1256
2.26-2.31	72.8	0.797	1262
2.22-2.26	77.4	0.816	1296
2.18-2.22	78.8	0.826	1324
2.14-2.18	82.1	0.775	1360
2.1-2.14	83.3	0.734	1490

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Processing

Software

Name	Version	Classification
MLPHARE		phasing
DM	6	phasing
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction
HKL-3000		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: 2.1→29.6 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.926 / WR_factor R_free: 0.244 / WR_factor R_work: 0.2 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.877 / SU B: 9.69 / SU ML: 0.122 / SU R Cruickshank DPI: 0.223 / SU R_free: 0.186 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.186 / Phase error: 31.2
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.242	1379	5 %	RANDOM
R_work	0.201	-	-	-
all	0.203	27351	-	-
obs	0.203	27351	99.64 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 64.88 Å² / B_iso mean: 24.376 Å² / B_iso min: 4.99 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.71 Å²	0 Å²	-1.31 Å²
2-	-	0.49 Å²	0 Å²
3-	-	-	-0.76 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→29.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3019	0	18	280	3317

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	3113
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2210
X-RAY DIFFRACTION	r_angle_refined_deg	1.319	2.002	4164
X-RAY DIFFRACTION	r_angle_other_deg	0.874	3	5434
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.904	5	388
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.2	25.401	137
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.589	15	651
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.385	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	472
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3346
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	566
X-RAY DIFFRACTION	r_mcbond_it	0.802	1.5	1902
X-RAY DIFFRACTION	r_mcbond_other	0.205	1.5	787
X-RAY DIFFRACTION	r_mcangle_it	1.496	2	3059
X-RAY DIFFRACTION	r_scbond_it	2.701	3	1211
X-RAY DIFFRACTION	r_scangle_it	4.378	4.5	1097

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.226	95	-
R_work	0.197	1893	-
all	-	1988	-
obs	-	-	99.8 %

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	0.5662	-1.5729	0.8019	4.9342	-2.2522	2.1259	-0.0882	-0.1967	-0.2094	0.0021	0.4088	0.5365	0.0082	-0.4584	-0.3207	0.1056	0.0441	0.0089	0.2982	-0.0042	0.3107	-27.7344	-19.4664	-21.7717
2	4.1887	-1.5044	1.1329	6.6279	1.7384	8.9929	-0.139	-0.8209	-0.2091	0.5974	0.0493	0.9208	0.222	-1.4548	0.0897	0.1365	-0.0151	0.0982	0.5148	0.0884	0.3311	-27.6502	-33.4656	-8.3725
3	0.3798	-0.9831	0.6781	6.3295	-4.3115	4.5217	-0.0835	-0.2313	-0.0452	0.0579	0.4399	0.3289	0.1624	-0.4387	-0.3564	0.1324	0.0282	0.0091	0.1802	0.0205	0.2244	-18.604	-26.9724	-18.7194
4	2.8323	-0.1636	-1.1365	1.9585	0.3757	7.8846	0.0018	-0.0166	0.1821	-0.2437	-0.1168	-0.0643	-0.4242	-0.1579	0.115	0.1454	0.0227	-0.0055	0.1701	-0.0317	0.0832	-18.3217	0.0145	-28.843
5	12.2324	-1.284	0.6984	1.496	1.5204	1.9865	0.2724	-1.0842	-1.1441	0.2017	-0.0162	-0.0728	0.2819	-0.3752	-0.2562	0.153	-0.0232	-0.0356	0.3654	0.0859	0.2093	-23.3428	-7.8103	-20.5675
6	5.7524	0.7202	1.2977	1.0976	-0.1808	4.5378	0.1486	-0.0499	-0.1535	-0.0582	-0.1329	-0.1748	0.1688	0.4522	-0.0157	0.1797	0.0357	0.0383	0.0947	0.0058	0.065	-50.2321	-8.1865	-26.56
7	5.5989	0.4575	-1.0485	4.2697	0.9834	11.7326	0.0214	0.2893	-0.0889	0.0026	-0.182	0.3568	1.0469	-0.5448	0.1606	0.1998	-0.0242	0.0097	0.0844	0.0026	0.0768	-62.3208	-9.3472	-29.7116
8	8.5751	0.6869	-0.6289	0.1252	0.0822	0.337	0.0107	0.0609	0.7588	0.0308	0.0696	0.0777	0.0468	0.0884	-0.0803	0.1545	0.0838	-0.01	0.1447	0.0233	0.1737	-36.8776	2.3551	-28.3471
9	3.2253	2.2735	5.1689	2.1162	4.0115	10.2793	0.2549	-0.3923	0.1044	0.4393	-0.3015	0.093	0.6048	-0.6078	0.0466	0.1747	-0.059	-0.0104	0.1253	-0.0011	0.0465	-4.4762	8.8056	2.6342
10	5.501	-1.4954	-4.3669	6.0118	2.9738	8.3365	0.1158	-0.0742	0.2007	0.1368	0.2891	-0.9456	0.0457	0.3102	-0.4049	0.0319	0	-0.0435	0.0493	-0.0579	0.1914	-3.0067	-1.7286	-20.6229
11	8.2587	-1.7414	0.8248	6.2276	0.8323	5.8888	0.0208	0.1859	-0.2247	0.1032	0.1995	-0.9841	0.2869	0.8345	-0.2204	0.0351	0.0677	-0.0481	0.1562	-0.098	0.3032	2.0549	-10.9451	-25.1529
12	1.2275	0.8661	1.0514	1.4811	1.7489	2.7599	-0.1611	0.0122	0.0295	-0.2519	-0.0527	0.0381	-0.3781	0.0678	0.2137	0.1187	-0.0086	-0.0229	0.0382	0.0343	0.0437	-3.1423	12.158	-12.9463

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	9 - 53
2	X-RAY DIFFRACTION	2	A	54 - 85
3	X-RAY DIFFRACTION	3	A	86 - 122
4	X-RAY DIFFRACTION	4	A	123 - 145
5	X-RAY DIFFRACTION	5	B	7 - 23
6	X-RAY DIFFRACTION	6	B	24 - 78
7	X-RAY DIFFRACTION	7	B	79 - 98
8	X-RAY DIFFRACTION	8	B	99 - 145
9	X-RAY DIFFRACTION	9	C	9 - 29
10	X-RAY DIFFRACTION	10	C	30 - 54
11	X-RAY DIFFRACTION	11	C	55 - 96
12	X-RAY DIFFRACTION	12	C	97 - 145

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