PDB-2f78: BenM effector binding domain with its effector benzoate

ID or keywords:

Entry

Database: PDB / ID: 2f78

Title

BenM effector binding domain with its effector benzoate

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

: / DNA-binding transcription factor activity /

Biological species

Acinetobacter baylyi (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 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 30, 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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PDBx/mmCIF format	2f78.cif.gz	119.3 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f7/2f78 ftp://data.pdbj.org/pub/pdb/validation_reports/f7/2f78	HTTPS FTP

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Related structure data

Related structure data	2f6gC 2f6pSC 2f7aC 2f7bC 2f7cC 2f8d 2f97 C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2f7a-d 2f6g-d 5ub9-d 2f8d-d 4mvf-d 2h9b-d 4ysm-2 4m0l-4 4yzb-1 4lq2-1 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

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	64.386, 69.508, 116.859
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-BEZ / BENZOIC ACID / Benzoic acid Mass: 122.121 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₇H₆O₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 588 / 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: 2.47 Å³/Da / Density % sol: 50.3 %
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: 1.00727 Å

Detector

Type: MARRESEARCH / Detector: CCD

Radiation

Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.00727 Å / Relative weight: 1

Refln sys abs

Index h	Index k	I	I/σ(I)	σ(I)
0	3	9.02	1.6	5.65
0	5	13.41	1.8	7.56
0	7	22.62	2.4	9.35
0	9	16.65	1.7	9.85
0	11	23.79	1.9	12.63
0	13	15.46	1.5	10.4
0	15	14.68	1.4	10.55
0	17	20.37	1.5	13.75
0	19	25.35	1.6	16.26
0	21	39.36	1.6	24.36
0	23	22.69	1.4	15.87
0	25	88.49	5.4	16.35
0	27	30.54	1.5	20.24
0	29	71.37	2.7	26.33
0	31	43.11	1.7	24.99
0	33	156.04	5.4	28.63
3	0	17.26	2.6	6.69
5	0	14.8	2.2	6.75
7	0	10.78	1.6	6.85
9	0	10.83	1.5	7.2
11	0	14.32	1.6	9
13	0	9.36	1.4	6.88
15	0	25.83	1.7	15.38
17	0	10.03	1.3	7.45
19	0	14.5	1.4	10.37
21	0	33.99	2	16.67
23	0	19.52	1.5	13.23
25	0	20.5	1.5	13.78
27	0	43.05	2.3	19.01
29	0	15.05	1.4	11.08
31	0	20.23	1.4	14.35

Reflection

Resolution: 2.05→59.761 Å / Num. all: 32511 / Num. obs: 32511 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / B_iso Wilson estimate: 27.01904 Å² / R_merge(I) obs: 0.068 / Net I/σ(I): 25.2

Reflection shell

Resolution: 2.05→2.12 Å / % possible obs: 97.5 % / R_merge(I) obs: 0.599 / Mean I/σ(I) obs: 3.8 / Num. measured obs: 3218 / Num. unique all: 3218 / Χ²: 1.959 / % possible all: 97.5

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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: 2.05→59.761 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.921 / WR_factor R_free: 0.236 / WR_factor R_work: 0.172 / SU B: 10.318 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.189 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2416	1635	5.08 %	RANDOM
R_work	0.1802	-	-	-
all	0.183	32187	-	-
obs	0.183	32187	95.706 %	-

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: 35.916 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.383 Å²	0 Å²	0 Å²
2-	-	1.737 Å²	0 Å²
3-	-	-	-2.12 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→59.761 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3471	0	45	588	4104

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	3691
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3697
X-RAY DIFFRACTION	r_angle_refined_deg	1.116	1.995	5021
X-RAY DIFFRACTION	r_angle_other_deg	0.928	3	8420
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.681	5	457
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.217	23.354	164
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.247	15	651
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.376	15	29
X-RAY DIFFRACTION	r_chiral_restr	0.137	0.2	567
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	4139
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	849
X-RAY DIFFRACTION	r_nbd_refined	0.185	0.2	726
X-RAY DIFFRACTION	r_nbd_other	0.167	0.2	4112
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	1778
X-RAY DIFFRACTION	r_nbtor_other	0.081	0.2	2270
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.131	0.2	431
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.151	0.2	13
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.206	0.2	82
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.128	0.2	35
X-RAY DIFFRACTION	r_mcbond_it	0.883	2	2941
X-RAY DIFFRACTION	r_mcbond_other	0.086	2	904
X-RAY DIFFRACTION	r_mcangle_it	1.317	5	3645
X-RAY DIFFRACTION	r_mcangle_other	0.559	5	3046
X-RAY DIFFRACTION	r_scbond_it	2.426	7	1635
X-RAY DIFFRACTION	r_scbond_other	0.87	7	3336
X-RAY DIFFRACTION	r_scangle_it	3.226	10	1367
X-RAY DIFFRACTION	r_scangle_other	1.347	10	5374

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 (%)
2.05-2.103	0.282	113	0.248	2168	0.25	2447	93.216
2.103-2.161	0.317	120	0.257	2156	0.26	2387	95.35
2.161-2.223	0.387	84	0.349	1862	0.351	2325	83.699
2.223-2.292	0.244	113	0.206	2099	0.208	2249	98.355
2.292-2.367	0.234	100	0.192	2058	0.194	2182	98.9
2.367-2.45	0.306	93	0.199	1984	0.204	2111	98.389
2.45-2.542	0.294	90	0.197	1922	0.201	2049	98.194
2.542-2.646	0.3	94	0.185	1851	0.19	1978	98.332
2.646-2.763	0.209	110	0.194	1748	0.194	1899	97.841
2.763-2.898	0.25	104	0.177	1686	0.181	1833	97.654
2.898-3.054	0.223	106	0.168	1586	0.172	1740	97.241
3.054-3.239	0.228	92	0.17	1491	0.173	1635	96.82
3.239-3.462	0.255	81	0.162	1415	0.166	1543	96.954
3.462-3.738	0.198	76	0.161	1334	0.163	1459	96.642
3.738-4.093	0.229	60	0.143	1235	0.147	1344	96.354
4.093-4.574	0.178	69	0.127	1104	0.13	1229	95.443
4.574-5.276	0.274	51	0.137	977	0.143	1085	94.747
5.276-6.449	0.212	32	0.192	844	0.193	938	93.39
6.449-9.068	0.208	32	0.176	657	0.177	743	92.732
9.068-59.761	0.259	15	0.178	375	0.18	455	85.714

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	4.7963	-0.9551	0.1587	2.9881	-0.2087	2.1245	0.0408	-0.1042	-0.1559	0.1207	0.0574	-0.1676	0.1278	0.0543	-0.0981	-0.2114	0.0302	-0.0036	-0.1391	-0.0359	-0.1716	57.675	53.505	61.03
2	3.6795	3.2887	0.5967	10.8881	-1.3005	2.0884	0.0972	-0.3934	-0.3319	0.2229	-0.0956	-0.3822	0.1568	0.1131	-0.0015	-0.199	0.0519	0.0167	-0.1044	-0.03	-0.1507	60.746	50.117	64.441
3	17.0773	-11.6602	-1.7226	14.4601	-0.8044	0.7774	0.5701	0.6348	0.7639	-0.7766	-0.1827	-0.8558	-0.3537	0.2298	-0.3875	-0.0948	0.0081	0.0406	-0.0119	-0.0354	-0.0441	70.216	61.354	52.952
4	10.9117	-3.6564	6.1698	3.4939	-4.263	5.6135	-0.3172	-0.1537	0.5725	0.0047	0.0652	-0.1977	-0.3852	0.2114	0.2519	-0.1655	0.027	-0.0344	-0.1263	-0.0575	-0.1483	64.178	59.19	54.64
5	11.8464	4.0231	-6.6057	9.4331	-4.9294	7.2107	0.4408	0.7696	1.2637	-0.5203	0.1053	0.8746	-1.0817	-0.6387	-0.5461	-0.0115	0.0924	0.0404	-0.0397	-0.0036	-0.0389	68.159	59.237	44.465
6	6.6196	-7.7916	-0.9803	10.0284	2.3029	2.2303	0.0879	0.0037	-0.1904	-0.2039	0.0306	0.2142	-0.099	-0.0238	-0.1185	-0.2211	-0.0105	0.002	-0.1658	0.0274	-0.1526	48.487	65.824	49.061
7	5.418	0.3925	0.6638	2.4326	1.4124	6.1778	0.0865	-0.0601	0.1771	-0.1603	0.0362	0.0862	-0.6518	-0.3532	-0.1228	-0.1347	0.0865	0.0298	-0.2077	0.0696	-0.1995	42.046	78.943	49.156
8	3.9968	-2.8062	4.9371	2.2919	-4.4768	9.6493	-0.0687	0.0915	0.1034	0.1536	0.1381	-0.3942	-0.7116	0.5215	-0.0693	-0.1282	-0.0482	0.0114	-0.0704	-0.0164	-0.1079	55.165	76.734	44.638
9	10.4932	-0.9467	3.1834	12.9878	-3.8397	11.8598	0.1164	0.1044	0.4391	-0.0863	0.1897	-0.448	-0.9699	0.9008	-0.3061	-0.1238	-0.0229	0.0705	-0.1737	-0.0936	-0.1782	52.938	81.245	56.06
10	2.8978	-0.6012	-0.3261	2.5475	1.4433	5.3124	-0.0034	-0.102	0.181	0.0825	0.2044	0.011	-0.372	-0.201	-0.2011	-0.1832	0.0342	-0.0004	-0.1246	0.0309	-0.1652	43.664	75.122	58.554
11	3.9998	-2.4042	0.6527	1.8158	-0.4877	0.7691	-0.1728	0.0369	0.0749	0.1113	0.1744	-0.0465	-0.1032	-0.0011	-0.0017	-0.1993	0.0113	0.0082	-0.1332	-0.0146	-0.1569	56.775	58.851	47.011
12	12.7455	-2.7621	3.0646	4.168	-1.8897	2.2678	0.1797	1.0825	-0.407	-0.1865	-0.0888	0.2596	0.2229	0.0398	-0.0909	-0.0398	0.0207	0.0016	0.0929	-0.039	0.0043	53.886	47.547	49.354
13	5.3694	-1.2654	2.035	3.698	-0.5955	3.0197	-0.0025	0.075	0.6398	-0.2435	0.0406	0.0986	-0.8181	-0.1849	-0.038	0.3581	0.0689	0.0962	0.131	-0.0351	0.1782	45.342	87.904	67.655
14	18.5928	-9.8572	-5.4697	29.8184	6.7891	9.3539	-0.0786	-0.3034	-0.1647	1.1601	0.1068	-1.8905	-1.7594	1.313	-0.0281	0.3763	-0.3408	0.2036	0.1755	-0.0519	-0.0491	59.45	90.728	77.856
15	0.3168	0.0893	-0.8019	7.5165	2.0061	2.9939	0.3191	-0.2163	0.1989	0.1492	0.0507	-0.3765	-0.8581	0.1777	-0.3697	0.2745	-0.0429	0.0545	0.1019	-0.0508	0.1515	49.642	80.262	80.715
16	7.5873	-0.2555	2.9903	10.0358	6.8069	6.2136	0.2021	-0.5066	-0.3335	0.581	0.225	-0.4073	0.5197	-0.004	-0.4272	-0.0823	-0.026	-0.0414	-0.1177	-0.0182	-0.1377	44.575	51.746	78.718
17	4.1624	-0.0535	-1.4829	3.3635	0.1264	5.25	-0.0007	-0.0766	-0.0304	0.0525	0.0876	-0.0687	0.0846	0.058	-0.0869	-0.2018	-0.0077	-0.037	-0.1364	-0.0524	-0.1877	51.294	59.879	81.364
18	18.1366	15.7594	2.4361	13.7045	1.7396	13.4645	-0.3682	0.2335	0.1334	-0.534	0.1356	-0.8426	-1.2715	1.3311	0.2325	-0.0264	-0.1361	0.0872	0.1061	-0.0638	0.136	61.089	74.01	78.806
19	1.0426	-1.4102	3.1298	4.6143	-3.118	11.0225	0.1079	-0.2934	0.2744	0.0242	0.2754	-0.1423	-0.202	0.426	-0.3833	-0.2183	-0.0056	0.0101	-0.0932	-0.0752	-0.1581	56.021	67.109	87.48
20	11.3494	-2.4661	-1.3522	13.5922	-14.5277	36.8801	-0.0409	-0.5622	-0.0543	0.7465	-0.1913	-0.533	-0.0689	1.8248	0.2322	-0.2951	0.0401	-0.0141	-0.0623	-0.1224	-0.1178	61.351	59.112	81.952
21	5.9221	3.0617	1.4097	1.7577	1.1645	1.4221	0.0228	0.017	0.2876	-0.1854	0.0035	-0.0268	-0.2039	0.0423	-0.0264	-0.1603	0.0006	0.0104	-0.0917	-0.0247	-0.1097	55.239	63.813	68.367
22	1.2483	0.098	-0.2927	0.9252	0.5599	3.6243	0.0189	-0.0192	0.0002	0.041	-0.0289	-0.1626	0.0639	-0.1491	0.0101	-0.2206	-0.0076	-0.0125	-0.1559	-0.0069	-0.1702	46.179	62.238	74.184
23	0.7143	3.3432	-2.5127	23.9662	-8.5033	10.1159	0.5951	-0.2485	0.2814	0.937	0.011	-0.4079	-1.9356	0.115	-0.606	0.2392	-0.0104	0.1833	-0.0613	-0.103	0.0733	48.337	84.961	82.802
24	21.2246	15.3715	-0.3239	41.7815	-5.3678	11.9411	0.8122	-1.0141	1.4045	2.0185	-0.7995	0.8878	-2.9997	-1.4153	-0.0127	0.4716	0.3809	0.2891	0.1139	-0.0925	-0.2204	37.615	89.693	77.642

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	87 - 112	7 - 32
2	2	A	A	113 - 126	33 - 46
3	3	A	A	127 - 137	47 - 57
4	4	A	A	138 - 147	58 - 67
5	5	A	A	148 - 155	68 - 75
6	6	A	A	156 - 170	76 - 90
7	7	A	A	171 - 198	91 - 118
8	8	A	A	199 - 218	119 - 138
9	9	A	A	219 - 228	139 - 148
10	10	A	A	229 - 258	149 - 178
11	11	A	A	259 - 280	179 - 200
12	12	A	A	281 - 308	201 - 228
13	13	B	B	90 - 128	10 - 48
14	14	B	B	129 - 138	49 - 58
15	15	B	B	139 - 170	59 - 90
16	16	B	B	171 - 177	91 - 97
17	17	B	B	178 - 198	98 - 118
18	18	B	B	199 - 203	119 - 123
19	19	B	B	204 - 216	124 - 136
20	20	B	B	217 - 223	137 - 143
21	21	B	B	224 - 236	144 - 156
22	22	B	B	237 - 262	157 - 182
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24	24	B	B	278 - 303	198 - 223

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