PDB-2f6g: BenM effector binding domain

ID or keywords:

Entry

Database: PDB / ID: 2f6g

Title

BenM effector binding domain

Components

HTH-type transcriptional regulator benM

Keywords

TRANSCRIPTION / LTTR / lysR-type transcriptional regulator / inducer binding domain / effector binding domain

Function / homology

Function and homology information

catabolic process / protein-DNA complex / DNA-binding transcription factor activity / DNA binding
Similarity search - Function

Biological species

Acinetobacter baylyi (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.908 Å

Authors

Clark, T. / Haddad, S. / Ezezika, O. / Neidle, E. / Momany, C.

Citation

Journal: J.Mol.Biol. / Year: 2007
Title: Distinct Effector-binding Sites Enable Synergistic Transcriptional Activation by BenM, a LysR-type Regulator.
Authors: Ezezika, O.C. / Haddad, S. / Clark, T.J. / Neidle, E.L. / Momany, C.

History

Deposition	Nov 29, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 31, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 18, 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
Revision 1.4	Aug 23, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2f6g.cif.gz	117.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2f6g.ent.gz	90.5 KB	Display	PDB format
PDBx/mmJSON format	2f6g.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2f6g_validation.pdf.gz	451.8 KB	Display	wwPDB validaton report
Full document	2f6g_full_validation.pdf.gz	455.9 KB	Display
Data in XML	2f6g_validation.xml.gz	24.4 KB	Display
Data in CIF	2f6g_validation.cif.gz	36.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f6/2f6g ftp://data.pdbj.org/pub/pdb/validation_reports/f6/2f6g	HTTPS FTP

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Related structure data

Related structure data	2f6pSC 2f78C 2f7aC 2f7bC 2f7cC 2f8d 2f97 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2f6p-d 2f7a-d 2f97-1 2f78-d 4br0-d 4yuq-1 4m0l-3 2h9b-d 4m0l-4 5tt6-d 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: HTH-type transcriptional regulator benM

B: HTH-type transcriptional regulator benM

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	64.412, 66.615, 116.549
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

The biological unit (effector binding domain) is the dimer in the asymmetric unit

#1: Protein	HTH-type transcriptional regulator benM / Ben and cat operon transcriptional regulator Mass: 26401.447 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baylyi (bacteria) / Strain: ADP1 / Gene: benM, benR / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O68014
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 579 / 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: 2.6 Å³/Da / Density % sol: 52.4 %
Crystal grow	Temperature: 288 K / Method: microbatch under oil Details: PEG 4000, ammonium sulfate, sodium acetate, NaCl, tris, glycerol, imidazole, microbatch under oil, temperature 288K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.97937 Å

Detector

Type: MARRESEARCH / Detector: CCD

Radiation

Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97937 Å / Relative weight: 1

Refln sys abs

Index h	Index k	Index l	I	I/σ(I)	σ(I)
0	0	11	17.16	2.2	7.75
0	0	13	10.13	1.5	6.63
0	0	15	7.02	1.4	5.09
0	0	17	6.68	1.4	4.91
0	0	19	14.1	1.6	8.61
0	0	21	13.79	1.6	8.81
0	0	23	7.26	1.3	5.4
0	0	25	7.03	1.3	5.26
0	0	27	8.3	1.3	6.18
0	0	29	7.56	1.3	5.66
0	0	31	11.32	1.4	8.13
0	0	33	33.18	2.5	13.48
0	0	35	17.48	1.5	11.33
0	0	37	9.52	1.3	7.06
0	0	39	11.18	1.4	8.11
0	0	45	8.67	1.3	6.45
0	0	47	11.26	1.4	8.14
0	3	0	8.61	1.6	5.53
0	5	0	10.78	1.5	6.99
0	7	0	9.48	1.4	6.67
0	9	0	10.18	1.4	7.25
0	11	0	13.7	1.5	9.43
0	17	0	14.47	1.3	10.83
0	19	0	14.02	1.3	10.4
0	23	0	15.76	1.4	11.56
0	25	0	19.87	1.4	13.71
0	27	0	28.28	1.5	19.16
3	0	0	8.53	1.5	5.63
5	0	0	9.93	1.5	6.78
7	0	0	27.39	2.6	10.49
9	0	0	16.02	1.5	10.85
11	0	0	16.55	1.5	10.74
13	0	0	11.65	1.4	8.53
15	0	0	13.67	1.4	9.92
17	0	0	18.53	1.4	12.99
19	0	0	30.35	1.6	18.41
21	0	0	24.18	1.5	16.17
23	0	0	21.65	1.5	14.76
25	0	0	19.21	1.4	13.63

Reflection

Resolution: 1.908→58.321 Å / Num. obs: 29271 / B_iso Wilson estimate: 27.81656 Å²

Reflection shell

Resolution (Å)	% possible obs (%)	R_merge(I) obs	Num. measured obs	Χ²	Diffraction-ID
1.9-1.97	22.5	0.434	878	0.814	1
1.97-2.05	34.9	0.197	1355	0.54	1
2.05-2.14	47.7	0.161	1874	0.667	1
2.14-2.25	62.5	0.112	2444	0.632	1
2.25-2.39	78.4	0.094	3054	0.707	1
2.39-2.58	98.2	0.084	3867	0.779	1
2.58-2.84	99.8	0.059	3950	0.803	1
2.84-3.25	100	0.04	3982	0.892	1
3.25-4.09	99.4	0.025	3986	0.96	1
4.09-50	93.3	0.019	3927	0.904	1

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	refmac_5.2.0005	refinement
PDB_EXTRACT	1.7	data extraction
HKL-2000		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB Entry 2F6P

2f6p

Resolution: 1.908→58.321 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.928 / WR_factor R_free: 0.232 / WR_factor R_work: 0.19 / SU B: 7.561 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.194 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.234	1461	4.998 %	Random
R_work	0.19	-	-	-
all	0.192	27770	-	-
obs	0.19004	27770	73.559 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 28.476 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.395 Å²	0 Å²	0 Å²
2-	-	2.568 Å²	0 Å²
3-	-	-	-2.173 Å²

Refinement step

Cycle: LAST / Resolution: 1.908→58.321 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3503	0	6	579	4088

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	3618
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3613
X-RAY DIFFRACTION	r_angle_refined_deg	1.226	1.981	4919
X-RAY DIFFRACTION	r_angle_other_deg	0.713	3	8229
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.937	5	445
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.409	23.519	162
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.968	15	636
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.923	15	26
X-RAY DIFFRACTION	r_chiral_restr	0.057	0.2	558
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	4029
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	813
X-RAY DIFFRACTION	r_nbd_refined	0.176	0.2	775
X-RAY DIFFRACTION	r_nbd_other	0.159	0.2	4065
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	1721
X-RAY DIFFRACTION	r_nbtor_other	0.079	0.2	2271
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.12	0.2	401
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.087	0.2	21
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.144	0.2	86
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.111	0.2	37
X-RAY DIFFRACTION	r_mcbond_it	0.893	2	2877
X-RAY DIFFRACTION	r_mcbond_other	0.067	2	884
X-RAY DIFFRACTION	r_mcangle_it	1.203	5	3595
X-RAY DIFFRACTION	r_mcangle_other	0.542	5	3016
X-RAY DIFFRACTION	r_scbond_it	2.1	7	1594
X-RAY DIFFRACTION	r_scbond_other	0.795	7	3227
X-RAY DIFFRACTION	r_scangle_it	2.79	10	1320
X-RAY DIFFRACTION	r_scangle_other	1.191	10	5213

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	% reflection obs (%)
1.908-1.958	0.32	34	0.301	517	0.302	2908	18.948
1.958-2.012	0.288	45	0.199	787	0.204	2810	29.609
2.012-2.07	0.269	49	0.191	1011	0.195	2730	38.828
2.07-2.133	0.265	73	0.19	1185	0.195	2655	47.382
2.133-2.203	0.27	57	0.194	1405	0.197	2608	56.058
2.203-2.281	0.248	97	0.184	1560	0.188	2500	66.28
2.281-2.367	0.242	87	0.187	1773	0.189	2425	76.701
2.367-2.463	0.297	112	0.196	2010	0.201	2338	90.761
2.463-2.572	0.257	103	0.203	2155	0.206	2260	99.912
2.572-2.698	0.277	109	0.201	2025	0.205	2140	99.72
2.698-2.843	0.274	85	0.192	1944	0.195	2038	99.558
2.843-3.015	0.225	97	0.2	1847	0.201	1947	99.846
3.015-3.223	0.229	88	0.188	1751	0.191	1842	99.837
3.223-3.48	0.267	98	0.185	1594	0.19	1699	99.588
3.48-3.811	0.206	76	0.174	1507	0.176	1597	99.123
3.811-4.258	0.204	73	0.166	1358	0.168	1444	99.1
4.258-4.913	0.178	57	0.161	1194	0.162	1284	97.43
4.913-6.006	0.165	57	0.201	1024	0.199	1101	98.183
6.006-8.45	0.24	43	0.23	794	0.23	881	95.006
8.45-58.321	0.328	21	0.276	329	0.279	531	65.913

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	1.1903	1.722	-0.448	20.6376	-5.6593	3.1335	-0.0023	-0.0265	0.2275	-0.1921	0.0356	0.0043	-0.2542	0.1504	-0.0332	0.097	0.0287	0.0202	0.2948	-0.1796	0.1245	23.492	57.059	32.088
2	6.2055	7.3802	-3.617	8.7773	-4.2887	4.3107	-0.0132	0.0127	-0.1014	-0.0571	-0.054	0.2173	0.0412	0.2566	0.0671	0.0741	0.0896	-0.036	0.1136	-0.0353	0.0303	25.871	38.409	38.28
3	9.7864	2.4329	-3.8041	3.7493	0.4967	8.691	-0.0398	0.2835	0.7402	-0.4553	0.2903	-0.1194	-0.0729	1.1747	-0.2505	0.0184	0.0156	-0.0248	0.0334	-0.0187	0.0312	28.383	22.783	34.214
4	7.5757	0.3558	-0.3496	3.3631	0.9193	7.1335	0.2888	-1.0989	-0.2444	-0.0398	-0.524	0.4942	0.5316	-1.1556	0.2351	0.2026	-0.0629	-0.1687	0.3429	-0.0874	0.2002	4.819	17.795	52.365
5	82.8238	-22.6803	3.1312	11.7805	1.6357	14.0234	-0.0084	0.0029	-0.0891	0.038	0.1074	-0.2134	0.2846	0.0235	-0.0989	0.0287	0.0016	-0.0063	0.0171	0.0045	0.0036	18.455	12.943	31.614
6	0.4688	-0.9636	-0.0029	9.355	2.5774	2.2703	0.1076	0.0141	0.0951	0.4873	-0.0324	-0.4704	0.2011	0.0937	-0.0751	0.0118	0.002	0.0153	0.059	0.0232	0.0211	16.959	45.152	43.888
7	1.1397	0.3954	-0.9758	2.4172	1.6482	6.7312	0.0711	0.1027	0.0958	-0.2075	0.2148	0.0055	-0.159	0.2106	-0.2859	0.019	-0.0195	0.0047	0.0201	-0.0054	0.0247	20.159	41.142	29.4
8	15.1163	15.7714	29.2718	19.4457	37.6094	73.3913	0.1519	-0.0342	0.2187	-0.0823	0.0405	0.0718	-0.1815	0.2141	-0.1925	0.0648	0.0254	-0.0065	0.0348	0.0329	0.0536	22.491	39.348	22.137
9	10.882	-7.9209	-0.8184	7.2981	3.4966	5.5526	-0.0305	-0.3587	-0.1671	-0.3069	-0.0513	-0.0364	-0.1763	-0.206	0.0817	0.1085	-0.0518	-0.0416	0.0999	-0.0424	0.0661	15.158	46.043	47.718
10	1.41	-1.0427	-0.6012	1.0388	0.983	2.7213	-0.0106	-0.1289	-0.0686	0.0064	0.1742	-0.0799	-0.0058	-0.0264	-0.1635	0.0079	0.0021	-0.006	0.009	0.0043	0.0092	10.054	42.39	48.138
11	1.2673	-3.2697	0.9494	24.1748	-5.6873	4.6029	-0.1455	0.0785	-0.1973	-0.2753	0.6726	0.7002	0.0716	-0.1526	-0.5272	0.0154	-0.0365	0.002	0.1107	-0.0316	0.0206	12.25	33.224	31.592
12	9.8224	3.9321	-2.4867	19.3106	-6.855	8.1397	0.1066	-0.6822	-1.6872	0.6251	-0.2705	0.3221	0.5891	-0.0592	0.164	0.0198	-0.0303	0.0047	0.0462	-0.0223	0.0866	7.312	11.233	46.335
13	2.9511	-0.114	0.6766	1.1867	0.4781	1.5746	0.0291	-0.1202	-0.0513	0.053	0.0102	0.0236	-0.0291	-0.0807	-0.0394	0.0283	0.0138	-0.0065	0.0191	-0.0047	0.0017	19.449	46.706	57.667
14	3.2137	-4.3572	1.7805	21.0196	-2.2855	0.9876	0.0594	0.0343	-0.2748	0.4145	0.1194	0.3342	-0.176	-0.0629	-0.1789	0.0094	-0.0068	-0.0057	0.0406	-0.0145	0.0108	29.273	42.631	55.788
15	3.3684	0.7541	1.5688	0.7047	0.8852	3.1019	-0.2615	0.1661	0.2845	-0.0415	0.0327	0.035	-0.2281	0.0593	0.2288	0.0351	-0.0278	-0.0301	0.0871	-0.0309	0.0719	30.713	55.336	58.436
16	7.007	10.3829	3.4523	15.8376	4.8972	1.8064	-0.0621	0.0361	-0.3368	-0.0158	0.0337	-0.4256	0.103	-0.1754	0.0285	0.0427	0.0387	0.0205	0.0398	0.0056	0.0519	28.055	50.98	72.527
17	5.3793	-10.3327	-6.3155	32.9358	21.5439	14.1842	0.1127	-0.1065	-0.0261	0.0968	0.0245	0.0575	-0.038	-0.0633	-0.1372	0.0186	-0.015	-0.0254	0.0384	0.0117	0.0383	6.638	15.739	58.724
18	5.5256	-2.5565	-5.7323	1.9296	1.6554	14.782	-0.3329	-0.629	0.2069	0.1768	0.6603	0.1694	1.1849	0.1877	-0.3273	0.0983	-0.0459	-0.0339	0.0208	-0.001	0.0893	7.039	24.928	79.955
19	10.429	6.7731	-7.7793	4.7549	-6.1713	9.3195	0.3754	0.1313	-0.2763	-0.1173	-0.1669	-0.2548	0.0408	-0.3195	-0.2086	0.2566	-0.004	-0.2088	0.1659	-0.0621	0.1961	3.139	13.27	89.638
20	0.2213	-1.4893	-1.8592	27.0538	37.5111	52.3143	-0.0936	0.1431	0.0444	-0.6033	0.25	-0.0739	0.3439	-0.3204	-0.1565	0.01	-0.0264	0.0264	0.2758	0.1203	0.2493	16.571	45.464	108.695
21	11.3661	0.1605	1.4641	4.1034	1.7219	14.5475	0.0876	-0.3683	0.7243	-0.1106	-0.0867	-0.0827	0.4533	-0.8785	-0.0009	0.0575	-0.0147	-0.0121	0.0363	-0.009	0.0066	11.215	26.792	58.406
22	1.3179	1.0394	-0.0628	1.0027	-0.1594	0.2177	-0.0462	0.123	-0.0098	-0.0166	0.0239	-0.0364	0.0022	0.0082	0.0222	0.0823	0.0769	0.0063	0.0883	-0.0076	0.1013	58.329	72.646	52.096
23	10.9096	3.2421	5.0292	2.875	1.6417	4.7004	0.1013	-0.4858	-0.3335	-0.0849	0.0012	-0.1746	0.0168	-0.2799	-0.1024	0.0053	0.007	0.0001	0.0136	-0.0044	0.0015	27.495	51.274	64.713
24	9.3318	0.0502	4.8619	9.7896	3.3066	16.354	0.0938	0.2312	1.0416	-1.1646	-0.2984	0.1767	-0.5991	-0.4565	0.2046	0.0692	0.0586	0.0396	0.0485	0.0131	0.1212	15.544	52.13	59.054

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	90 - 99	10 - 19
2	2	A	A	100 - 112	20 - 32
3	3	A	A	113 - 140	33 - 60
4	4	A	A	141 - 149	61 - 69
5	5	A	A	150 - 156	70 - 76
6	6	A	A	157 - 176	77 - 96
7	7	A	A	177 - 216	97 - 136
8	8	A	A	217 - 221	137 - 141
9	9	A	A	222 - 234	142 - 154
10	10	A	A	235 - 259	155 - 179
11	11	A	A	260 - 279	180 - 199
12	12	A	A	280 - 305	200 - 225
13	13	B	B	87 - 112	7 - 32
14	14	B	B	113 - 128	33 - 48
15	15	B	B	129 - 157	49 - 77
16	16	B	B	158 - 170	78 - 90
17	17	B	B	171 - 178	91 - 98
18	18	B	B	179 - 199	99 - 119
19	19	B	B	200 - 213	120 - 133
20	20	B	B	214 - 220	134 - 140
21	21	B	B	221 - 241	141 - 161
22	22	B	B	242 - 275	162 - 195
23	23	B	B	276 - 289	196 - 209
24	24	B	B	290 - 308	210 - 228

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