PDB-2f97: Effector Binding Domain of BenM (crystals generated from high pH ...

ID or keywords:

Entry

Database: PDB / ID: 2f97

Title

Effector Binding Domain of BenM (crystals generated from high pH conditions)

Components

HTH-type transcriptional regulator benM

Keywords

GENE REGULATION / BenM / LysR-type regulator / tetramerization / effector binding domain / inducer 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: 2.2 Å

Authors

Ezezika, O.C. / Haddad, S. / Neidle, E.L. / Momany, C.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Oligomerization of BenM, a LysR-type transcriptional regulator: structural basis for the aggregation of proteins in this family.
Authors: Ezezika, O.C. / Haddad, S. / Neidle, E.L. / Momany, C.

History

Deposition	Dec 5, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 19, 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 30, 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	2f97.cif.gz	68 KB	Display	PDBx/mmCIF format
PDB format	pdb2f97.ent.gz	49 KB	Display	PDB format
PDBx/mmJSON format	2f97.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2f97_validation.pdf.gz	453.8 KB	Display	wwPDB validaton report
Full document	2f97_full_validation.pdf.gz	454.8 KB	Display
Data in XML	2f97_validation.xml.gz	13.3 KB	Display
Data in CIF	2f97_validation.cif.gz	19.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f9/2f97 ftp://data.pdbj.org/pub/pdb/validation_reports/f9/2f97	HTTPS FTP

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Related structure data

Related structure data	2f8dC 2f6gS 2f6p 2f78 2f7a 2f7b 2f7c S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2f6g-d 2h9b-d 2f6p-d 1j4b-d 2f7a-d 2f78-d 5ub9-d 3pjw-d 1kjz-d 2h99-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: HTH-type transcriptional regulator benM

hetero molecules

27.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: HTH-type transcriptional regulator benM

hetero molecules

A: HTH-type transcriptional regulator benM

hetero molecules

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

Unit cell

Length a, b, c (Å)	70.048, 70.048, 187.683
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	95
Space group name H-M	P4₃22

Components on special symmetry positions

ID	Model	Components
1	1	A-1040- HOH

Details

The biological assembly is a dimer generated from the monomer in the asymmetric unit by applying the crystallographic symmetry operation -x, y,-z.

#1: Protein	HTH-type transcriptional regulator benM / Ben and cat operon transcriptional regulator Mass: 26401.447 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baylyi (bacteria) / Strain: ADP1 / Gene: benM, benR / Plasmid: pET21B / Production host: Escherichia coli (E. coli) / Strain (production host): DE3(BL21) / References: UniProt: O68014
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 252 / 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: 4.36 Å³/Da / Density % sol: 71.77 %
Crystal grow	pH: 9 Details: PEG 8000, TAPS, LiCl, imidazole, tris, NaCl, cis,cis-muconate, glycerol, pH 9, Microbatch under oil

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / 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: 2.2→70.014 Å / Num. all: 24724 / Num. obs: 24724 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.9 % / B_iso Wilson estimate: 43.75363 Å² / R_merge(I) obs: 0.063 / Net I/σ(I): 65.96
Reflection shell	Resolution: 2.2→2.28 Å / % possible obs: 99.9 % / R_merge(I) obs: 0.769 / Mean I/σ(I) obs: 5.92 / Num. measured obs: 2381 / Num. unique all: 2381 / Χ²: 1.258 / % possible all: 99.9

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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 2F6G

2f6g

Resolution: 2.2→70.014 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.954 / WR_factor R_free: 0.202 / WR_factor R_work: 0.171 / SU B: 6.52 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.14 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2094	1218	4.969 %	RANDOM
R_work	0.1763	-	-	-
all	0.1779	23294	-	-
obs	0.1779	23294	99.582 %	-

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: 42.296 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.223 Å²	0 Å²	0 Å²
2-	-	0.223 Å²	0 Å²
3-	-	-	-0.447 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→70.014 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1722	0	44	252	2018

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	1846
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	23
X-RAY DIFFRACTION	r_angle_refined_deg	0.915	1.996	2495
X-RAY DIFFRACTION	r_angle_other_deg	0.309	3	50
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.812	5	225
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.267	23.875	80
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.528	15	320
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.525	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.057	0.2	278
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	1373
X-RAY DIFFRACTION	r_nbd_refined	0.162	0.2	851
X-RAY DIFFRACTION	r_nbd_other	0.097	0.2	24
X-RAY DIFFRACTION	r_nbtor_refined	0.295	0.2	1265
X-RAY DIFFRACTION	r_nbtor_other	0.075	0.2	4
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.099	0.2	191
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.152	0.2	54
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.217	0.2	1
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.1	0.2	33
X-RAY DIFFRACTION	r_mcbond_it	0.515	2	1155
X-RAY DIFFRACTION	r_mcangle_it	1.072	5	1813
X-RAY DIFFRACTION	r_mcangle_other	0.023	5	3
X-RAY DIFFRACTION	r_scbond_it	2.099	7	779
X-RAY DIFFRACTION	r_scbond_other	0.099	7	23
X-RAY DIFFRACTION	r_scangle_it	3.242	10	682
X-RAY DIFFRACTION	r_scangle_other	0.416	10	47

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 (%)
2.2-2.258	0.306	86	0.242	1625	0.245	1781	96.07
2.258-2.319	0.256	90	0.205	1609	0.207	1700	99.941
2.319-2.387	0.225	95	0.195	1606	0.197	1701	100
2.387-2.46	0.229	93	0.2	1535	0.202	1630	99.877
2.46-2.54	0.227	78	0.192	1517	0.194	1596	99.937
2.54-2.63	0.179	80	0.19	1468	0.189	1550	99.871
2.63-2.729	0.244	77	0.193	1405	0.196	1483	99.933
2.729-2.84	0.226	72	0.186	1381	0.188	1454	99.931
2.84-2.966	0.231	59	0.19	1325	0.192	1385	99.928
2.966-3.11	0.236	67	0.18	1252	0.182	1319	100
3.11-3.278	0.251	62	0.171	1211	0.175	1274	99.922
3.278-3.477	0.182	55	0.159	1151	0.16	1207	99.917
3.477-3.716	0.188	54	0.154	1087	0.155	1142	99.912
3.716-4.013	0.232	45	0.151	1026	0.154	1074	99.721
4.013-4.394	0.152	50	0.141	935	0.141	985	100
4.394-4.911	0.126	39	0.152	865	0.151	905	99.89
4.911-5.666	0.22	36	0.165	767	0.167	803	100
5.666-6.928	0.273	42	0.21	662	0.214	704	100
6.928-9.75	0.193	24	0.176	541	0.176	567	99.647
9.75-70.014	0.205	14	0.278	326	0.275	355	95.775

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	12.7714	-3.0005	3.7733	4.8933	-3.4545	6.1801	0.0414	0.9866	0.0051	-0.2401	0.0111	0.3117	0.0516	-0.3357	-0.0524	-0.1784	0.0136	-0.0172	0.1153	0.0201	-0.0323	14.847	26.624	-4.153
2	3.2913	-0.7757	0.2296	2.6535	-0.0681	3.7175	-0.1124	0.3522	-0.224	-0.0904	0.0214	0.0413	0.2962	-0.1827	0.0911	-0.1227	-0.0446	0.0245	0.0217	0.0012	-0.0309	19.5	15.676	-1.48
3	2.4072	-1.0521	-0.0035	4.0503	-0.4539	3.3054	-0.1343	0.3108	0.1645	-0.0629	0.1122	0.0415	-0.2612	-0.2966	0.022	-0.1819	0.0098	-0.0192	0.0521	0.046	-0.0418	15.985	27.804	0.054
4	5.693	-0.7818	6.6716	2.4971	0.2883	8.4255	-0.4786	-0.0876	-0.1042	0.8069	0.3919	0.2971	-0.6824	-0.2222	0.0867	0.0011	0.1372	-0.0065	0.1616	-0.0092	-0.0279	13.003	31.253	14.044
5	6.4853	-2.132	0.6286	1.319	-0.0326	1.4216	-0.2559	-0.2744	-0.3668	0.1844	0.1384	0.0583	0.349	-0.0057	0.1175	0.0057	0.0428	0.0311	-0.0162	0.0616	-0.0379	33.32	11.198	15.508
6	2.613	-0.0688	0.6723	3.3739	-1.7364	5.3761	-0.1497	-0.197	0.1057	0.4634	0.1105	-0.1459	-0.1066	0.3204	0.0392	-0.0851	0.0707	-0.0015	0.0095	0.0097	-0.0615	38.826	19.505	18.727
7	8.4812	-10.2871	2.9821	14.9217	-0.0269	6.3217	-0.1353	0.3285	0.4585	0.2174	-0.0277	-0.2271	-0.4168	-0.0362	0.1631	-0.0603	0.0606	-0.016	0.0117	0.0482	0.0249	29.146	29.499	11.24
8	0.0706	-0.5995	0.1755	6.0767	-4.7176	11.007	-0.1246	-0.1555	0.1777	0.432	0.2504	0.1815	-0.1801	-0.1606	-0.1257	-0.007	0.0904	0.0103	0.0167	0.0008	-0.0429	30.991	23.356	22.067
9	1.9328	0.0527	-0.6612	3.5037	-0.8133	4.4695	-0.0655	-0.0661	0.2937	0.1833	0.092	-0.0372	-0.1677	0.2414	-0.0265	-0.1191	0.0302	-0.019	-0.0058	0.0049	-0.0237	41.016	23.411	10.807
10	2.0484	-0.1877	-0.3636	1.2369	0.1643	2.8247	-0.1558	-0.1064	-0.1937	0.067	0.046	0.0236	0.3304	0.0236	0.1099	-0.047	0.0341	0.0128	-0.0367	0.0422	-0.0416	35.227	12.891	12.307
11	15.4661	-6.9214	7.7277	7.5059	-3.0213	5.7545	-0.4495	-0.2699	0.5757	0.462	0.0438	0.0086	-0.1922	-0.7696	0.4056	-0.1449	0.0258	0.0287	0.0899	-0.0042	-0.0556	10.374	26.24	8.439
12	12.592	-5.4235	4.0993	10.4245	-2.0083	3.8881	-0.1057	0.2119	-0.2173	-0.0716	0.1165	0.6445	0.1532	-0.6534	-0.0107	-0.1991	-0.0607	-0.0065	0.2572	-0.012	0.0224	5.008	20.993	0.9
13	6.3539	-4.077	-2.5497	10.946	-5.096	10.6229	-0.2597	0.3418	-0.9128	0.3962	0.2068	0.9332	0.5301	-1.0321	0.0529	-0.1123	-0.1185	0.0393	0.0981	-0.0018	0.0772	11.053	11.105	4.028
14	7.9356	-3.5073	-6.5431	26.6616	0.6413	9.0383	-0.4354	0.0726	-1.2085	0.6133	-0.1079	1.0119	0.881	-0.6399	0.5434	-0.0801	-0.1176	0.0386	0.0183	0.0108	0.0599	12.477	8.56	8.77

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Auth seq-ID	Label seq-ID
1	1	89 - 98	9 - 18
2	2	99 - 113	19 - 33
3	3	114 - 147	34 - 67
4	4	148 - 155	68 - 75
5	5	156 - 180	76 - 100
6	6	181 - 198	101 - 118
7	7	199 - 203	119 - 123
8	8	204 - 216	124 - 136
9	9	217 - 236	137 - 156
10	10	237 - 268	157 - 188
11	11	269 - 277	189 - 197
12	12	278 - 286	198 - 206
13	13	287 - 294	207 - 214
14	14	295 - 304	215 - 224

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