PDB-2f6p: BenM effector binding domain- SeMet derivative

ID or keywords:

Entry

Database: PDB / ID: 2f6p

Title

BenM effector binding domain- SeMet derivative

Components

HTH-type transcriptional regulator benM

Keywords

GENE REGULATION / LTTR / lysR-type transcriptional regulator / inducer binding domain / effector binding domain

Function / homology

Function and homology information

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

Biological species

Acinetobacter baylyi (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.001 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2f6p.cif.gz	113.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2f6p.ent.gz	93 KB	Display	PDB format
PDBx/mmJSON format	2f6p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2f6p_validation.pdf.gz	456.2 KB	Display	wwPDB validaton report
Full document	2f6p_full_validation.pdf.gz	458.1 KB	Display
Data in XML	2f6p_validation.xml.gz	23 KB	Display
Data in CIF	2f6p_validation.cif.gz	34.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f6/2f6p ftp://data.pdbj.org/pub/pdb/validation_reports/f6/2f6p	HTTPS FTP

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Related structure data

Related structure data	2f6gC 2f78C 2f7aC 2f7bC 2f7cC 2f8d 2f97 C: citing same article (ref.)
Similar structure data	2f6g-d 2f7a-d 2f97-1 2h9b-d 4m0l-3 4br0-d 1wao-2 4ysm-1 4m0l-4 4yzb-1 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

53.6 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)	65.090, 66.702, 117.849
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: 26682.818 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.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 487 / 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: 22-ID / Wavelength: 0.97935 Å
Detector	Type: MARRESEARCH / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97935 Å / Relative weight: 1
Reflection	Resolution: 2→58.926 Å / Num. obs: 35252 / % possible obs: 99.6 % / Redundancy: 11.4 % / B_iso Wilson estimate: 24.31766 Å² / R_merge(I) obs: 0.069 / Net I/σ(I): 49.6
Reflection shell	Resolution: 2→2.07 Å / % possible obs: 98.6 % / R_merge(I) obs: 0.221 / Mean I/σ(I) obs: 9.6 / Num. measured obs: 3427 / Num. unique all: 3427 / Χ²: 0.696 / % possible all: 98.6

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Phasing

Phasing

Method:

SAD

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	26.948	0.81	0.092	0.088	0.234
2	Se	38.188	0.246	0.591	0.186	0.291
3	Se	19.844	0.949	0.111	0.183	0.233
4	Se	29.895	0.855	0.705	0.244	0.265
5	Se	36.783	0.424	0.396	0.146	0.281
6	Se	37.589	0.485	0.838	0.131	0.207
7	Se	32.522	0.85	0.836	0.027	0.288
8	Se	37.339	0.02	0.07	0.033	0.141
9	Se	52.147	0.418	0.717	0.146	0.14

Phasing dm

FOM : 0.54 / FOM acentric: 0.55 / FOM centric: 0.52 / Reflection: 33118 / Reflection acentric: 29880 / Reflection centric: 3238

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
5.7-21.031	0.86	0.89	0.76	1587	1186	401
3.6-5.7	0.85	0.87	0.75	4745	4047	698
2.9-3.6	0.74	0.75	0.62	5833	5197	636
2.5-2.9	0.58	0.59	0.44	5566	5095	471
2.1-2.5	0.39	0.4	0.29	9598	8922	676
2-2.1	0.23	0.23	0.15	5789	5433	356

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.02	phasing
RESOLVE	2.02	phasing
REFMAC	refmac_5.2.0005	refinement
PDB_EXTRACT	1.7	data extraction
HKL-2000		data reduction

Refinement

Method to determine structure:

SAD / Resolution: 2.001→58.926 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.931 / WR_factor R_free: 0.225 / WR_factor R_work: 0.18 / SU B: 7.084 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.161 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2267	1743	4.956 %	Random
R_work	0.1811	-	-	-
all	0.183	33427	-	-
obs	0.183	35170	99.451 %	-

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: 26.413 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.688 Å²	0 Å²	0 Å²
2-	-	-0.832 Å²	0 Å²
3-	-	-	-2.856 Å²

Refinement step

Cycle: LAST / Resolution: 2.001→58.926 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3532	0	15	487	4034

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	3651
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3640
X-RAY DIFFRACTION	r_angle_refined_deg	1.048	1.98	4961
X-RAY DIFFRACTION	r_angle_other_deg	0.719	3	8293
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.792	5	446
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.062	23.598	164
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.523	15	641
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.747	15	25
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	561
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	4054
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	819
X-RAY DIFFRACTION	r_nbd_refined	0.178	0.2	688
X-RAY DIFFRACTION	r_nbd_other	0.163	0.2	3825
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	1729
X-RAY DIFFRACTION	r_nbtor_other	0.079	0.2	2205
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.116	0.2	301
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.119	0.2	10
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.208	0.2	83
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.166	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	0.732	2	2222
X-RAY DIFFRACTION	r_mcbond_other	0.069	2	889
X-RAY DIFFRACTION	r_mcangle_it	1.55	5	3615
X-RAY DIFFRACTION	r_mcangle_other	0.697	5	3034
X-RAY DIFFRACTION	r_scbond_it	2.541	7	1459
X-RAY DIFFRACTION	r_scbond_other	0.701	7	2902
X-RAY DIFFRACTION	r_scangle_it	3.831	10	1343
X-RAY DIFFRACTION	r_scangle_other	1.731	10	5259

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 (%)
2.001-2.053	0.234	127	0.187	2371	0.19	2559	97.616
2.053-2.109	0.227	131	0.178	2386	0.18	2527	99.604
2.109-2.17	0.212	113	0.171	2328	0.173	2446	99.796
2.17-2.237	0.241	109	0.174	2253	0.177	2366	99.831
2.237-2.31	0.205	117	0.174	2185	0.175	2309	99.697
2.31-2.391	0.227	115	0.182	2109	0.185	2230	99.731
2.391-2.481	0.258	109	0.19	2029	0.194	2141	99.86
2.481-2.582	0.224	93	0.182	1992	0.184	2090	99.761
2.582-2.697	0.234	106	0.192	1886	0.194	1996	99.8
2.697-2.828	0.242	80	0.181	1833	0.183	1918	99.739
2.828-2.981	0.264	95	0.189	1709	0.193	1811	99.613
2.981-3.161	0.246	79	0.185	1646	0.187	1726	99.942
3.161-3.379	0.234	80	0.19	1548	0.192	1629	99.939
3.379-3.648	0.214	94	0.178	1435	0.18	1529	100
3.648-3.995	0.229	64	0.167	1343	0.17	1409	99.858
3.995-4.464	0.192	57	0.161	1230	0.162	1288	99.922
4.464-5.15	0.204	58	0.163	1092	0.165	1153	99.74
5.15-6.295	0.217	51	0.214	925	0.214	976	100
6.295-8.852	0.235	40	0.209	732	0.21	779	99.101
8.852-58.926	0.237	25	0.189	395	0.191	482	87.137

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	3.6191	-1.5356	-0.9462	3.0366	-0.8993	1.2863	-0.0076	0.0761	-0.0472	0.1322	0.285	0.1842	-0.0953	0.0415	-0.2773	-0.0382	-0.0025	0.0107	0.0092	0.0226	-0.0052	22.482	39.727	43.684
2	19.1776	5.0501	-7.3383	22.9875	5.06	5.0656	-0.5352	0.1323	0.485	-0.8197	-0.1215	0.8167	0.4149	-0.4519	0.6567	0.01	-0.001	-0.0019	0.0114	0.0021	-0.0002	39.429	37.958	36.352
3	1.6388	-2.2034	0.613	3.1064	0.1859	7.315	-0.2656	0.0747	-0.3243	0.0558	0.1056	-0.4273	-0.2301	0.0373	0.1601	-0.0037	0.0171	0.0025	-0.0276	0.0458	0.0013	34.994	27.332	44.766
4	8.6527	-0.09	-3.5082	3.0821	0.6699	5.2687	-0.0558	0.5311	0.5105	-0.3274	0.1435	-0.1056	-0.118	-0.0541	-0.0876	0.0269	-0.0068	-0.041	0.0746	0.0128	0.0626	36.111	34.164	42.767
5	16.9696	-13.361	3.7351	57.4631	-16.0456	17.2134	-0.2282	-0.4405	1.3319	0.7765	0.6587	0.044	-1.1993	0.6665	-0.4304	0.0283	0.0102	0.0132	0.0438	-0.0129	0.0071	37.351	32.169	55.244
6	17.1643	-2.0287	1.4123	0.8355	0.1196	4.0523	0.0779	-0.3956	0.5331	-0.1867	0.1319	0.0465	-0.0618	-0.0639	-0.2097	-0.0475	-0.036	-0.0061	-0.0199	0	-0.015	20.701	37.341	52.946
7	8.3496	-5.6477	3.2289	4.3474	-2.2774	4.1633	0.2404	0.1065	-0.0314	-0.1989	-0.0584	0.1666	0.2785	0.0501	-0.182	-0.0259	-0.0085	-0.0125	-0.0452	0.0193	0.0064	8.08	32.159	47.622
8	2.4189	0.0687	0.384	0.8906	-0.7346	6.1635	0.1638	-0.2304	0.0156	-0.0051	0.0169	0.0058	0.2979	-0.0425	-0.1808	-0.0307	-0.026	-0.0236	-0.0319	0.0088	-0.0077	9.271	28.404	58.466
9	8.7962	9.4868	21.3093	11.1735	24.0632	52.8634	0.0239	-0.4763	-0.0866	-0.2887	0.5968	-0.2348	0.0819	-0.9363	-0.6207	0.012	0.0012	0.0267	0.0529	0.0086	0.0619	8.277	27.738	66.012
10	20.2787	10.0611	-17.3863	27.3993	-11.7167	27.855	0.7308	0.4429	1.3038	-0.0087	0.031	-0.2783	-0.0097	1.1139	-0.7617	0.0181	0.0126	-0.0365	0.0225	-0.0013	0.0262	13.817	24.238	42.172
11	8.126	-0.2428	4.792	4.577	-7.8507	15.8257	-0.0316	-0.2956	0.2955	0.3469	-0.2268	-0.0576	-0.9054	-0.4213	0.2585	0.0417	-0.0204	-0.0104	-0.0012	-0.0299	-0.0123	8.293	33.043	42.987
12	1.5448	-0.0499	0.2464	0.782	-0.6013	3.9689	0.092	0.0884	0.0267	-0.1101	-0.0566	0.0155	-0.1391	0.1561	-0.0354	-0.0188	0.0077	-0.0056	-0.0277	-0.0005	0.0034	11.47	38.325	41.234
13	7.7043	-1.3392	-2.1519	1.7556	0.1277	3.7193	-0.0003	-0.0357	-0.3065	0.2256	0.0349	-0.0024	-0.142	-0.1851	-0.0346	0.0075	0.0155	0.0026	-0.0117	-0.0029	-0.0112	22.014	33.995	53.183
14	7.1082	-3.8931	-5.0204	6.7236	1.8361	6.246	0.0932	0.1747	-0.1804	-0.8339	-0.4985	-0.2249	-0.1223	-0.3555	0.4054	0.1285	-0.0562	0.0257	0.0436	0.0438	0.2266	40.005	35.47	35.558
15	3.1352	-0.0957	0.0227	3.6933	0.4346	2.8318	-0.0121	0.071	0.0252	-0.0058	0.0308	-0.2135	-0.2068	0.0566	-0.0188	-0.0459	-0.0044	-0.0251	-0.0163	-0.0186	0.009	7.316	26.685	29.488
16	17.502	-5.2456	-3.9593	32.1293	-8.4866	16.5628	-0.1892	0.2311	1.0198	0.7389	-0.5716	-1.7252	-1.1612	0.1257	0.7608	0.0318	0.0141	0.0117	0.0405	-0.0173	0.0048	-3.761	26.529	35.792
17	4.8372	-3.1381	-0.4469	3.5099	1.1593	8.3051	0.3183	0.3429	-0.0214	-0.3357	-0.3008	-0.4146	-0.4737	0.3428	-0.0176	0.0144	-0.0016	-0.017	0.0043	0.0015	0.017	11.27	18.812	25.251
18	3.46	0.7054	-0.1911	2.6386	-0.7142	3.3503	0.011	-0.1046	0.2481	0.1774	0.1527	0.0834	-0.1955	-0.2575	-0.1636	0.0106	0.017	-0.0218	0.0399	0.0148	0.0233	-0.101	20.937	28.352
19	3.3856	1.2691	0.7937	4.2322	1.5677	0.6155	-0.1699	0.1133	0.2744	-0.0277	0.0104	0.3698	0.0187	0.1679	0.1594	-0.0055	-0.0339	-0.0018	0.0093	0.0084	0.0031	-2.632	20.565	16.857
20	10.5218	7.2779	4.835	5.5237	3.5412	5.4227	0.4535	0.0962	-0.0793	0.3219	-0.1346	-0.1326	0.4119	0.1159	-0.3189	-0.0178	0.0014	-0.0168	-0.0183	-0.0047	-0.0071	23.216	35.574	24.292
21	24.3922	-10.9355	15.0069	5.9372	-4.2047	15.3862	-0.282	0.2191	-0.0754	0.1892	0.4858	0.0723	0.1086	0.812	-0.2039	0.0492	-0.0414	0.0376	0.0164	-0.0264	0.0465	34.445	42.463	27.58
22	1.1046	0.4641	-0.3245	1.0279	0.0838	2.5427	-0.0278	0.1342	-0.0079	-0.0259	0.1132	0.0419	0.0469	0.0409	-0.0855	-0.086	-0.0137	0.0088	0.0197	-0.0026	0.0052	20.45	31.681	14.04
23	37.9433	20.0064	-39.4904	13.7963	-23.3111	43.0082	1.0808	-0.5542	1.3178	0.3952	0.0067	0.649	0.1997	0.9823	-1.0875	0.0056	0.0026	-0.0155	0.005	-0.0039	0.0049	30.192	27.496	24.486
24	3.0149	6.1232	4.1158	15.8238	7.0607	6.1164	-0.3884	-0.0546	0.3795	-0.0277	0.0512	1.1089	-0.3977	0.2825	0.3373	0.0448	-0.003	0.0175	0.0219	-0.0037	0.0007	24.329	37.685	30.843
25	0.7912	0.1623	-0.4303	0.9286	-0.0498	0.6166	-0.0151	0.1243	0.0003	0.0344	0.0478	0.0741	0.0478	-0.0393	-0.0327	-0.028	-0.0231	0.007	-0.0001	0.0028	-0.001	7.1	31.433	29.447
26	1.0213	1.4123	-0.1123	2.2802	-0.2929	0.096	0.1412	-0.0665	0.1384	0.2663	-0.0744	0.161	-0.0398	0.0516	-0.0668	0.0087	-0.0055	0.0042	0.0148	0.0033	0.0127	-13.994	2.294	29.848
27	0.9902	1.5376	1.1126	4.3823	3.7036	3.2076	-0.1753	0.036	-0.1748	-0.3699	0.4168	0.0512	-0.2723	0.1196	-0.2416	-0.021	-0.0284	-0.0079	-0.0345	-0.0339	-0.0018	0.492	18.7	20.056
28	4.4488	-0.0505	-0.4639	4.4931	-0.1809	5.2709	-0.0055	-0.6301	-0.211	0.1081	-0.0065	0.3495	-0.3278	-0.2542	0.0121	0.0198	0.0372	-0.031	0.1183	0.0403	0.2226	-5.469	31.45	34.075

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 - 112	10 - 32
2	2	A	A	113 - 121	33 - 41
3	3	A	A	122 - 138	42 - 58
4	4	A	A	139 - 149	59 - 69
5	5	A	A	150 - 156	70 - 76
6	6	A	A	157 - 163	77 - 83
7	7	A	A	164 - 177	84 - 97
8	8	A	A	178 - 216	98 - 136
9	9	A	A	217 - 221	137 - 141
10	10	A	A	222 - 226	142 - 146
11	11	A	A	227 - 237	147 - 157
12	12	A	A	238 - 266	158 - 186
13	13	A	A	267 - 281	187 - 201
14	14	A	A	282 - 307	202 - 227
15	15	B	B	87 - 112	7 - 32
16	16	B	B	113 - 121	33 - 41
17	17	B	B	122 - 128	42 - 48
18	18	B	B	129 - 148	49 - 68
19	19	B	B	149 - 161	69 - 81
20	20	B	B	162 - 170	82 - 90
21	21	B	B	171 - 178	91 - 98
22	22	B	B	179 - 219	99 - 139
23	23	B	B	220 - 225	140 - 145
24	24	B	B	226 - 238	146 - 158
25	25	B	B	239 - 259	159 - 179
26	26	B	B	260 - 275	180 - 195
27	27	B	B	276 - 289	196 - 209
28	28	B	B	290 - 308	210 - 228

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