PDB-5hpf: Crystal Structure of the Double Mutant of PobR Transcription Fact...

ID or keywords:

Entry

Database: PDB / ID: 5hpf

Title

Crystal Structure of the Double Mutant of PobR Transcription Factor Inducer Binding Domain from Acinetobacter

Components

p-hydroxybenzoate hydroxylase transcriptional activator

Keywords

TRANSCRIPTION / Transcription factor / ligand binding domain

Function / homology

Function and homology information

3,4-dihydroxybenzoate metabolic process / catabolic process / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding
Similarity search - Function

Biological species

Acinetobacter baylyi str. ADP1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.309 Å

Authors

Kim, Y. / Tesar, C. / Jedrejczak, R. / Jha, R. / Strauss, C.E.M. / Joachimiak, A.

Funding support

United States, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2016
Title: A microbial sensor for organophosphate hydrolysis exploiting an engineered specificity switch in a transcription factor.
Authors: Jha, R.K. / Kern, T.L. / Kim, Y. / Tesar, C. / Jedrzejczak, R. / Joachimiak, A. / Strauss, C.E.

History

Deposition	Jan 20, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 7, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Jun 6, 2018	Group: Data collection / Database references / Source and taxonomy Category: citation / citation_author / entity_src_gen Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Dec 25, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5hpf.cif.gz	227 KB	Display	PDBx/mmCIF format
PDB format	pdb5hpf.ent.gz	184.6 KB	Display	PDB format
PDBx/mmJSON format	5hpf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hp/5hpf ftp://data.pdbj.org/pub/pdb/validation_reports/hp/5hpf	HTTPS FTP

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Related structure data

Related structure data	5hpiC C: citing same article (ref.)
Similar structure data	3b21-d 1ore-d 4hjv-2 3w30-1 3uwk-2 4qn8-2 4nyh-3 5a0x-2 3w42-2 2xs6-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

5hpiC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#183 - Mar 2015 Phototropin similarity (1) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (1)

Deposited unit

A: p-hydroxybenzoate hydroxylase transcriptional activator

B: p-hydroxybenzoate hydroxylase transcriptional activator

C: p-hydroxybenzoate hydroxylase transcriptional activator

hetero molecules

60.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: p-hydroxybenzoate hydroxylase transcriptional activator

hetero molecules

defined by author&software
20.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: p-hydroxybenzoate hydroxylase transcriptional activator

hetero molecules

defined by author&software
20 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: p-hydroxybenzoate hydroxylase transcriptional activator

hetero molecules

defined by author&software
20.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	111.348, 111.348, 282.174
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	97
Space group name H-M	I422

#1: Protein	p-hydroxybenzoate hydroxylase transcriptional activator Mass: 19956.459 Da / Num. of mol.: 3 / Mutation: delta-L141, L220V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baylyi str. ADP1 (bacteria) Gene: pobR, ACIAD1718 / Plasmid: pMCSG68 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: Q43992
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.67 Å³/Da / Density % sol: 66.48 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.1 M sodium/potassium phosphate pH 5.6

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 12, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97934 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. obs: 37742 / % possible obs: 99.8 % / Redundancy: 5 % / B_iso Wilson estimate: 46.7 Å² / R_merge(I) obs: 0.121 / Net I/σ(I): 13.2
Reflection shell	Resolution: 2.3→2.34 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.849 / % possible all: 96.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.10pre_2104: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing
SBC-Collect		data collection

Refinement

Method to determine structure:

SAD / Resolution: 2.309→40.375 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.16 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2152	1874	4.97 %
R_work	0.1702	-	-
obs	0.1724	37742	95.73 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 58.7 Å²

Refinement step

Cycle: LAST / Resolution: 2.309→40.375 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4128	0	57	118	4303

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4262
X-RAY DIFFRACTION	f_angle_d	0.925	5814
X-RAY DIFFRACTION	f_dihedral_angle_d	15.163	2583
X-RAY DIFFRACTION	f_chiral_restr	0.054	703
X-RAY DIFFRACTION	f_plane_restr	0.005	741

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.3089-2.3714	0.2791	118	0.225	2548	X-RAY DIFFRACTION	90
2.3714-2.4411	0.2729	119	0.1992	2782	X-RAY DIFFRACTION	98
2.4411-2.5199	0.2158	148	0.1919	2772	X-RAY DIFFRACTION	98
2.5199-2.61	0.2855	148	0.2113	2753	X-RAY DIFFRACTION	98
2.61-2.7144	0.2688	145	0.2068	2794	X-RAY DIFFRACTION	97
2.7144-2.838	0.2832	148	0.2222	2759	X-RAY DIFFRACTION	97
2.838-2.9875	0.2434	138	0.2036	2774	X-RAY DIFFRACTION	97
2.9875-3.1746	0.2514	149	0.1953	2768	X-RAY DIFFRACTION	97
3.1746-3.4196	0.229	149	0.1839	2762	X-RAY DIFFRACTION	96
3.4196-3.7635	0.2509	167	0.1649	2753	X-RAY DIFFRACTION	96
3.7635-4.3076	0.1855	147	0.1428	2761	X-RAY DIFFRACTION	95
4.3076-5.425	0.1633	141	0.1321	2795	X-RAY DIFFRACTION	95
5.425-40.3811	0.1778	157	0.1611	2847	X-RAY DIFFRACTION	92

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	9.2545	-1.9486	-1.0458	8.9821	0.7053	8.8959	-0.1166	0.2501	-0.9215	0.6478	-0.1168	0.1298	1.0314	-0.062	0.2037	0.4442	-0.0499	-0.007	0.2952	0.0088	0.3881	10.885	-24.6194	55.8096
2	3.5055	2.1549	1.6542	4.7955	0.0348	1.0436	-0.1723	0.5299	-0.3528	-0.201	0.0107	-0.0895	0.2096	-0.0067	0.1321	0.3564	0.021	0.0463	0.37	0.0027	0.2637	11.5885	-21.5261	46.0789
3	5.765	1.0531	2.0783	5.3223	-0.4372	4.2478	-0.2783	0.2973	-0.2604	-0.4356	0.085	-0.0203	0.4008	0.3984	0.1576	0.3985	0.0529	0.1091	0.3479	-0.0076	0.3508	20.9024	-17.0256	43.3218
4	7.0867	1.3046	2.9855	4.2719	0.2999	7.9518	0.072	0.5942	0.1316	-0.5199	-0.3781	-1.2808	0.453	1.6536	0.1348	0.3548	0.1265	0.1379	0.6677	0.173	0.6567	36.9696	-13.8805	40.9629
5	2.8681	-4.3259	1.5777	6.6952	-1.9631	2.0696	0.3244	1.048	0.2914	-0.5191	-0.5831	-0.5413	-0.1094	0.4278	0.2735	0.5232	0.0398	0.112	0.5952	0.0877	0.3917	24.2257	-5.7383	34.8543
6	8.4832	1.5753	-4.8559	6.9926	-2.9173	3.8579	-0.0706	-0.3707	0.4128	0.0776	-0.2583	-0.7268	-0.5999	1.44	0.3538	0.352	-0.0372	-0.0328	0.432	0.0847	0.4856	31.1085	-5.731	48.186
7	1.4662	-1.2948	0.2139	4.6036	-2.6333	3.7915	0.0693	0.1754	0.0356	-0.1863	-0.1254	-0.0649	0.106	0.1131	0.062	0.2308	0.012	0.0034	0.3063	-0.0048	0.34	15.84	-11.0423	49.6116
8	4.2978	-3.9244	-1.4928	3.5721	0.9066	7.3579	-0.4556	-0.8502	-0.3496	0.8647	0.0139	-0.0413	0.1719	0.8366	0.3969	0.2714	0.0098	0.052	0.4483	0.0815	0.3865	17.3553	-18.0627	61.3132
9	0.649	1.3822	0.8605	5.5946	-1.2319	4.5905	-0.4231	0.5952	-0.1013	-0.5099	0.1716	-0.7051	0.1918	1.3184	0.2528	0.6835	-0.0433	0.1202	0.9434	-0.0535	0.4314	26.9255	-0.4079	6.6387
10	1.4889	0.1702	-0.3565	4.7728	1.4695	0.5615	0.0222	-0.0844	0.1172	0.4601	-0.1842	-0.238	-0.1365	0.2316	0.1154	0.6198	0.0382	-0.0308	0.8742	0.0485	0.3397	24.3628	-2.3273	16.4078
11	2.6499	1.0376	-0.2018	5.886	1.267	5.2575	0.0291	-0.3101	-0.1376	0.9085	-0.075	-0.1054	0.5099	0.5962	-0.0171	0.5751	0.0647	-0.0578	0.6962	0.0336	0.4098	23.7998	-12.6509	18.9876
12	8.5992	3.2837	2.5881	2.8956	1.1511	2.2645	-0.0893	-0.4708	-1.3336	0.7718	-0.2381	-1.5791	1.3972	0.7703	0.1662	1.2577	0.4104	-0.251	0.9004	0.1339	1.0666	27.5306	-28.6452	21.1202
13	5.2619	-1.4688	-1.0883	7.6966	-0.6143	0.4314	0.2094	-0.0475	-0.4382	0.2936	-0.2099	-0.2086	0.4707	0.043	0.0408	0.7365	0.0457	-0.1081	0.7125	0.0454	0.4031	15.4918	-20.4014	19.6545
14	1.0462	0.0084	1.1782	2.6475	-0.4355	2.3516	0.2787	0.2754	-0.214	-0.5175	-0.3993	-0.2776	0.5325	0.6594	0.1265	0.716	0.2139	0.0173	0.7573	-0.0099	0.3733	24.7506	-13.8221	7.9378
15	9.1044	-3.3138	-3.2086	3.2852	0.2588	1.5059	-0.1069	-0.6497	0.1782	0.4307	0.2356	-0.1817	0.0918	0.6339	-0.1318	0.6438	0.0477	0.0171	0.6615	-0.0402	0.2995	13.3415	-6.8229	12.5182
16	1.993	-0.9233	-1.7554	2.1058	0.8928	9.5396	-0.1057	1.0806	-0.3682	-0.8457	-0.4382	-0.6432	1.1667	0.5278	0.4806	0.7027	0.1846	0.0706	0.7208	0.0241	0.4602	23.4791	-8.9759	1.1796
17	7.1548	2.4255	-1.8168	4.6083	-2.1654	3.8616	-0.0033	-0.3267	-0.5796	0.2879	-0.09	-0.0041	0.1765	0.3398	0.088	0.3123	0.0402	-0.0027	0.3254	0.0773	0.3919	7.8215	-25.279	74.5335
18	3.963	0.9343	-0.8489	2.8	-0.4344	2.0523	-0.0166	-0.2791	-0.201	0.1419	-0.0478	-0.0418	0.1097	-0.0674	0.0477	0.2997	-0.0265	-0.0071	0.2776	0.0383	0.3783	-5.6206	-23.8212	77.732

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 96 through 113 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 114 through 143 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 144 through 170 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 171 through 181 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 182 through 193 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 194 through 207 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 208 through 255 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 256 through 271 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 96 through 113 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 114 through 143 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 144 through 170 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 171 through 181 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 182 through 193 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 194 through 207 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 208 through 255 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 256 through 271 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 96 through 138 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 139 through 271 )

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