PDB-2f7a: BenM effector binding domain with its effector, cis,cis-muconate

ID or keywords:

Entry

Database: PDB / ID: 2f7a

Title

BenM effector binding domain with its effector, cis,cis-muconate

Components

HTH-type transcriptional regulator benM

Keywords

GENE REGULATION /

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

muconate

Function / homology

Function and homology information

aromatic compound catabolic process / DNA-binding transcription factor activity /

Biological species

Acinetobacter baylyi (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 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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Download

PDBx/mmCIF format	2f7a.cif.gz	115.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2f7a.ent.gz	88.5 KB	Display	PDB format
PDBx/mmJSON format	2f7a.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f7/2f7a ftp://data.pdbj.org/pub/pdb/validation_reports/f7/2f7a	HTTPS FTP

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Related structure data

Related structure data	2f6gC 2f6pSC 2f78C 2f7bC 2f7cC 2f8d 2f97 C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2f78-d 2f6g-d 2f6p-d 4yzb-1 4m0l-4 6qz2-2 4m2l-d 4ysm-1 4lq2-1 6qz2-8 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

53.3 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)	64.741, 65.777, 117.974
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

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Protein , 1 types, 2 molecules AB

#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

#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

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Non-polymers , 5 types, 486 molecules

#2: Chemical	ChemComp-BEZ / BENZOIC ACID / Benzoic acid Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₆O₂
#3: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-CCU / (2Z,4Z)-HEXA-2,4-DIENEDIOIC ACID / CIS,CIS-MUCONIC ACID / Muconic acid Mass: 142.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₆O₄
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.38 Å³/Da / Density % sol: 48.26 %
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	Index l	I	I/σ(I)	σ(I)
0	0	3	2.76	1.5	1.87
0	0	13	10.34	1.7	6.15
0	0	15	15.2	2	7.47
0	0	17	7.61	1.4	5.34
0	0	19	15.67	2	7.93
0	0	21	14.84	1.8	8.15
0	0	23	6.76	1.3	5.01
0	0	25	11.32	1.6	7.3
0	0	27	13.83	1.7	8.07
0	0	29	16.35	1.8	9.01
0	0	35	10.69	1.4	7.53
0	0	37	12.13	1.5	8.27
0	0	39	10.31	1.4	7.25
0	0	41	11.07	1.5	7.44
0	0	43	18.86	1.8	10.36
0	0	45	11.81	1.5	8.03
0	0	47	16.3	1.7	9.49
0	0	49	10.45	1.4	7.39
0	0	51	10.49	1.4	7.56
0	0	55	9.32	1.3	6.94
0	0	57	16.43	1.6	10.19
0	0	59	17.02	1.7	10.31
0	0	61	12.51	1.4	8.69
0	3	0	4.59	1.5	3.14
0	5	0	10.22	1.9	5.27
0	7	0	9.58	1.6	6
0	9	0	12.47	1.7	7.25
0	11	0	13.28	1.6	8.36
0	13	0	11.36	1.4	8.04
0	15	0	11.52	1.5	7.91
0	19	0	14.34	1.5	9.84
0	21	0	14.13	1.4	9.81
0	23	0	13.11	1.4	9.1
0	25	0	14.85	1.5	10
0	27	0	22.22	1.8	12.18
0	31	0	26.94	1.5	17.89
0	33	0	36.43	1.6	22.4
0	35	0	27.13	1.6	17.33
3	0	0	6.29	1.5	4.11
5	0	0	5.6	1.4	4.04
7	0	0	13.48	1.7	8.1
9	0	0	7.92	1.4	5.75
11	0	0	22.12	2.2	9.96
13	0	0	16.52	1.6	10.05
15	0	0	14.09	1.4	9.77
17	0	0	19.45	1.5	13.1
19	0	0	16.21	1.5	11.14
21	0	0	16.66	1.5	11.2
23	0	0	21.47	1.6	13.75
25	0	0	16.77	1.4	11.95
27	0	0	34.36	1.9	17.67
31	0	0	27.22	1.5	18.45
33	0	0	21.66	1.4	15.59

Reflection

Resolution: 1.5→59.028 Å / Num. all: 54680 / Num. obs: 54680 / % possible obs: 59.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.46 % / B_iso Wilson estimate: 24.51076 Å² / R_merge(I) obs: 0.053 / Net I/σ(I): 25.8

Reflection shell

Resolution: 1.49→1.55 Å / % possible obs: 0 % / R_merge(I) obs: 0 / Mean I/σ(I) obs: 0.3 / Num. measured obs: 0 / Num. unique all: 53 / % possible all: 0.6

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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: 1.9→59.028 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.924 / WR_factor R_free: 0.252 / WR_factor R_work: 0.206 / SU B: 9.3 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.174 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2503	1788	4.993 %	RANDOM
R_work	0.207	-	-	-
all	0.209	35808	-	-
obs	0.209	35808	88.526 %	-

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: 30.727 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.556 Å²	0 Å²	0 Å²
2-	-	1.313 Å²	0 Å²
3-	-	-	-1.869 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→59.028 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3517	0	37	481	4035

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	3649
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	3643
X-RAY DIFFRACTION	r_angle_refined_deg	1.094	1.992	4953
X-RAY DIFFRACTION	r_angle_other_deg	0.74	3.002	8291
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.434	5	443
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.341	23.5	160
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.188	15	636
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.683	15	25
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	563
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	4055
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	824
X-RAY DIFFRACTION	r_nbd_refined	0.181	0.2	759
X-RAY DIFFRACTION	r_nbd_other	0.169	0.2	3888
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	1737
X-RAY DIFFRACTION	r_nbtor_other	0.079	0.2	2226
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.146	0.2	340
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.09	0.2	20
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.173	0.2	96
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.136	0.2	24
X-RAY DIFFRACTION	r_mcbond_it	1.037	2	2885
X-RAY DIFFRACTION	r_mcbond_other	0.097	2	892
X-RAY DIFFRACTION	r_mcangle_it	1.475	5	3611
X-RAY DIFFRACTION	r_mcangle_other	0.65	5	3025
X-RAY DIFFRACTION	r_scbond_it	2.662	7	1610
X-RAY DIFFRACTION	r_scbond_other	1.023	7	3258
X-RAY DIFFRACTION	r_scangle_it	3.565	10	1340
X-RAY DIFFRACTION	r_scangle_other	1.527	10	5266

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 (%)
1.9-1.949	0.407	115	0.342	2401	0.345	2930	85.87
1.949-2.003	0.332	150	0.259	2697	0.263	2867	99.302
2.003-2.061	0.264	131	0.216	2669	0.219	2800	100
2.061-2.124	0.279	144	0.219	2557	0.222	2704	99.889
2.124-2.194	0.386	110	0.304	2283	0.307	2650	90.302
2.194-2.27	0.388	62	0.297	975	0.302	2555	40.587
2.27-2.356	0.275	91	0.218	1636	0.221	2462	70.146
2.356-2.452	0.21	113	0.214	2269	0.214	2382	100
2.452-2.561	0.294	123	0.206	2162	0.211	2285	100
2.561-2.686	0.228	119	0.205	2068	0.207	2189	99.909
2.686-2.831	0.267	92	0.203	1988	0.206	2080	100
2.831-3.002	0.246	90	0.196	1893	0.198	1983	100
3.002-3.209	0.235	89	0.193	1776	0.195	1865	100
3.209-3.465	0.243	91	0.183	1664	0.186	1756	99.943
3.465-3.794	0.222	27	0.167	455	0.17	1600	30.125
3.794-4.24	0.27	40	0.16	984	0.164	1473	69.518
4.24-4.891	0.18	72	0.147	1230	0.149	1310	99.389
4.891-5.981	0.187	68	0.186	1050	0.186	1121	99.732
5.981-8.415	0.159	42	0.198	847	0.196	899	98.888
8.415-59.028	0.277	19	0.259	416	0.26	538	80.855

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	1.958	0.7572	-0.1487	1.7292	0.2489	1.2895	-0.1273	0.1422	-0.0323	-0.132	0.0572	0.1514	0.0728	0.0198	0.0701	-0.0746	0.0085	0.0042	-0.0617	0.0081	0.0173	36.923	16.761	-4.217
2	38.086	-9.7111	11.2242	9.5038	2.3132	8.5092	0.0711	0.3801	-0.5455	-0.9387	-0.1043	0.0466	0.0121	-0.1862	0.0331	-0.0179	-0.0137	0.0768	-0.1353	-0.0578	-0.031	37.016	9.346	-7.292
3	1.7471	0.0111	-2.3059	14.5353	1.5108	6.7282	0.1359	0.1458	0.3046	0.019	0.0347	0.4788	-0.553	-0.5205	-0.1706	-0.1223	0.0685	-0.0221	-0.0986	0.0269	0.0136	31.202	25.835	-0.718
4	7.2753	2.2957	-0.6774	2.057	0.4878	3.1482	0.1682	-0.2022	0.4623	0.166	-0.0516	0.2428	-0.1371	-0.0814	-0.1165	-0.0956	0.012	-0.0071	-0.0669	-0.0035	0.0366	29.166	24.305	6.071
5	12.7126	-0.3052	-2.337	2.9715	1.2209	0.8874	0.3898	0.1522	0.0095	0.251	-0.393	0.0323	0.1246	-0.0863	0.0033	-0.1025	-0.046	-0.0109	0.0444	0.0563	-0.0429	34.416	20.7	12.247
6	6.304	7.2527	-3.3132	9.9232	-5.453	6.1248	0.3443	-0.1727	-0.284	0.5297	-0.3872	-0.3026	-0.7004	0.2636	0.0428	-0.0172	-0.0537	-0.0248	-0.0531	-0.0096	-0.0419	54.875	38.789	6.951
7	0.487	0.4046	-0.2552	0.8268	-0.055	1.5184	0.0366	-0.0992	-0.1209	0.0374	-0.0183	-0.0325	-0.2989	-0.0171	-0.0183	-0.0823	0.0308	-0.0106	-0.067	0.0021	-0.0537	45.401	31.092	7.936
8	0.2932	0.5661	0.199	1.5772	0.5497	1.9312	-0.0209	-0.0864	-0.0199	-0.1771	0.002	-0.0446	-0.6553	-0.2721	0.0189	0.104	0.13	-0.0073	-0.042	-0.0123	-0.1016	45.672	47.345	-16.14
9	16.3802	-3.889	5.3747	4.2906	-3.7455	23.3153	0.5052	0.5106	0.0023	-1.0854	-0.6008	0.0849	1.0422	0.9981	0.0956	0.0843	0.1031	0.0079	-0.1113	-0.0093	-0.0786	53.674	16.266	-20.915
10	1.2117	-1.0379	-0.489	3.7891	-0.3463	5.1514	0.0356	-0.1308	-0.1218	-0.3674	0.1149	0.3565	0.1454	-0.3034	-0.1506	-0.1216	-0.0402	-0.0242	-0.0598	0.0351	-0.0755	42.332	25.855	-23.427
11	0.952	-1.0701	-0.5985	1.5037	-0.4828	4.817	-0.1377	0.0495	0.1481	-0.2298	0.3887	-0.0006	0.363	-0.8306	-0.2509	-0.0735	-0.0807	-0.0285	0.0412	0.0237	-0.0548	38.78	27.039	-27.079
12	3.6672	-4.6147	3.3348	11.1043	-6.768	4.4501	-0.3411	-0.4596	-0.1834	0.7091	0.6057	0.3891	-0.3373	-0.2283	-0.2646	-0.0633	0.0603	0.0109	0.0604	0.0345	-0.0755	41.614	28.503	-10.331
13	0.1709	-0.0045	0.1448	1.6492	-0.6844	1.9996	-0.0425	-0.105	0.0134	-0.0638	0.0842	0.0058	-0.1407	-0.0465	-0.0416	-0.0694	0.0043	0.0138	-0.0498	0.0033	-0.0335	48.722	33.222	-19.194
14	9.2858	-3.4874	-1.7078	11.2116	3.3208	9.4918	0.0257	0.642	0.3362	-0.8345	0.2559	-0.6806	-2.0094	0.7598	-0.2815	0.2851	-0.1125	0.1143	-0.2095	0.0622	-0.2126	55.562	53.307	-19.913

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	84 - 112	4 - 32
2	2	A	A	113 - 121	33 - 41
3	3	A	A	122 - 131	42 - 51
4	4	A	A	132 - 151	52 - 71
5	5	A	A	152 - 160	72 - 80
6	6	A	A	161 - 174	81 - 94
7	7	A	A	175 - 311	95 - 231
8	8	B	B	90 - 171	10 - 91
9	9	B	B	172 - 178	92 - 98
10	10	B	B	179 - 204	99 - 124
11	11	B	B	205 - 224	125 - 144
12	12	B	B	225 - 235	145 - 155
13	13	B	B	236 - 276	156 - 196
14	14	B	B	277 - 302	197 - 222

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 486 molecules

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-Yorodumi

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Movie

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Structure viewers

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This page

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Open data

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Validation report

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Assembly

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 486 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi