PDB-4fqt: Structure of AgamOBP1 Bound to 6-methyl-5-hepten-2-one

ID or keywords:

Entry

Database: PDB / ID: 4fqt

Title

Structure of AgamOBP1 Bound to 6-methyl-5-hepten-2-one

Components

Anopheles Gambiae Odorant Binding protein 1

Keywords

Odorant-Binding Protein / Odorant Binding Protein

Function / homology

Function and homology information

odorant binding / response to stimulus / sensory perception of smell
Similarity search - Function

Biological species

Anopheles gambiae (African malaria mosquito)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.2 Å

Authors

Murphy, E.J. / Booth, J.C.

Citation

Journal: J.Biol.Chem. / Year: 2013
Title: Interactions of Anopheles gambiae Odorant-binding Proteins with a Human-derived Repellent: IMPLICATIONS FOR THE MODE OF ACTION OF N,N-DIETHYL-3-METHYLBENZAMIDE (DEET).
Authors: Murphy, E.J. / Booth, J.C. / Davrazou, F. / Port, A.M. / Jones, D.N.

History

Deposition	Jun 25, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 2, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jan 9, 2013	Group: Database references
Revision 1.2	Jan 23, 2013	Group: Database references
Revision 1.3	Mar 20, 2013	Group: Database references
Revision 1.4	Dec 27, 2023	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	4fqt.cif.gz	162.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4fqt.ent.gz	133.4 KB	Display	PDB format
PDBx/mmJSON format	4fqt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4fqt_validation.pdf.gz	453.2 KB	Display	wwPDB validaton report
Full document	4fqt_full_validation.pdf.gz	455.2 KB	Display
Data in XML	4fqt_validation.xml.gz	14.4 KB	Display
Data in CIF	4fqt_validation.cif.gz	19.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fq/4fqt ftp://data.pdbj.org/pub/pdb/validation_reports/fq/4fqt	HTTPS FTP

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Related structure data

Similar structure data	3ogn-1 4i4y-3 4i4y-5 1dk7-1 4i4p-3 4nwy-2 5wq0-5 5i4c-d 4i4r-4 4i4r-3 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Anopheles Gambiae Odorant Binding protein 1

B: Anopheles Gambiae Odorant Binding protein 1

hetero molecules

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

1

A: Anopheles Gambiae Odorant Binding protein 1

hetero molecules

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

2

B: Anopheles Gambiae Odorant Binding protein 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	32.769, 68.993, 64.552
Angle α, β, γ (deg.)	90.00, 104.71, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Anopheles Gambiae Odorant Binding protein 1 / Odorant-binding protein AgamOBP1 Mass: 14547.619 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anopheles gambiae (African malaria mosquito) Strain: PEST Gene: AgamOBP1, AgaP_AGAP003309, agCG48275, OBP17, OBPjj83b AgaP_AGAP010409 Plasmid: Pet28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I8T0
#2: Chemical	ChemComp-0VT / 6-methylhept-5-en-2-one / 6-methyl-5-hepten-2-one Mass: 126.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₄O
#3: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.43 Å³/Da / Density % sol: 49.29 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 298 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 4.2.2 / Wavelength: 1 Å

Detector

Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 12, 2010

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Redundancy: 3.17 % / Number: 84462 / R_merge(I) obs: 0.151 / Χ²: 1 / D res high: 1.57 Å / D res low: 46.26 Å / Num. obs: 26439 / % possible obs: 68.4

Diffraction reflection shell

ID: 1

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	R_merge(I) obs	Chi squared	Redundancy	Rejects
3.38	46.26	99.3	0.074	0.92	3.74	235
2.69	3.38	99.7	0.101	0.9	3.79	170
2.35	2.69	100	0.187	0.99	3.79	42
2.13	2.35	100	0.319	1.06	3.75	71
1.98	2.13	96.1	0.615	1.18	2.94	92
1.86	1.98	76.9	0.616	1	2.22	17
1.77	1.86	53.7	0.699	0.93	2	3
1.69	1.77	34.3	0.651	0.94	1.82	3
1.63	1.69	17.9	0.642	1.19	1.56	1
1.57	1.63	3.8	0.75	2.62	1.16

Reflection

Resolution: 1.57→46.26 Å / Num. obs: 26439 / % possible obs: 68.4 % / Redundancy: 3.17 % / R_merge(I) obs: 0.151 / Net I/σ(I): 4.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.57-1.63	1.16	0.75	0.3	1	3.8
1.63-1.69	1.56	0.642	0.4	1	17.9
1.69-1.77	1.82	0.651	0.4	1	34.3
1.77-1.86	2	0.699	0.5	1	53.7
1.86-1.98	2.22	0.616	0.7	1	76.9
1.98-2.13	2.94	0.615	1	1	96.1
2.13-2.35	3.75	0.319	2.1	1	100
2.35-2.69	3.79	0.187	4	1	100
2.69-3.38	3.79	0.101	7	1	99.7
3.38-46.26	3.74	0.074	11.4	1	99.3

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	46.26 Å

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Processing

Software

Name	Version	Classification
d*TREK	9.7L	data scaling
d*TREK	9.7L	data reduction
PHASER	2.1.4	phasing
PHENIX	1.8_1069	refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→31.697 Å / Occupancy max: 1 / Occupancy min: 0.03 / SU ML: 0.25 / σ(F): 0 / Phase error: 32.76 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2386	717	5.1 %
R_work	0.1849	-	-
obs	0.1877	14069	99.06 %

Solvent computation

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

Displacement parameters

B_iso mean: 32.2783 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→31.697 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2032	0	44	178	2254

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2185
X-RAY DIFFRACTION	f_angle_d	1.413	2939
X-RAY DIFFRACTION	f_dihedral_angle_d	16.038	849
X-RAY DIFFRACTION	f_chiral_restr	0.079	303
X-RAY DIFFRACTION	f_plane_restr	0.01	380

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 (%)
2.2001-2.3699	0.3682	120	0.2984	2611	X-RAY DIFFRACTION	97
2.3699-2.6083	0.2886	144	0.1936	2663	X-RAY DIFFRACTION	100
2.6083-2.9855	0.218	140	0.1971	2710	X-RAY DIFFRACTION	100
2.9855-3.7604	0.2514	160	0.1762	2658	X-RAY DIFFRACTION	99
3.7604-31.7006	0.1941	153	0.1515	2710	X-RAY DIFFRACTION	99

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	2.1607	-2.2511	-1.2237	5.878	-1.1939	5.9028	0.0892	0.0458	-1.0649	-0.1029	-0.0419	-0.0938	0.2484	-0.2489	0.0986	0.215	-0.0465	-0.0091	0.176	-0.0159	0.2886	5.1317	-3.4411	24.911
2	6.079	1.7724	-0.7726	1.086	0.896	3.9765	0.4873	0.5409	-0.5115	0.1539	-0.012	-0.8853	0.6417	0.298	-0.4914	0.1958	0.0413	-0.0919	0.2678	-0.0751	0.2996	18.1781	2.315	25.2652
3	6.0299	-2.9574	-3.845	8.4233	0.2376	6.2666	-0.0507	-0.1848	-0.3158	0.6076	0.0614	-0.4138	-0.3724	0.8235	-0.0947	0.1734	-0.0978	-0.0624	0.304	0.0093	0.2516	17.7106	13.3481	34.0202
4	3.5733	2.6292	0.9031	3.1383	1.9183	5.2001	0.3798	-0.6587	-0.2173	1.1208	-0.3659	0.0433	0.5059	-0.7375	-0.2154	0.3469	-0.0188	-0.0083	0.197	0.0143	0.2366	2.9157	9.2975	35.4202
5	2.57	0.1635	-0.4678	2.0472	-0.3081	4.1692	0.2154	-0.0828	0.1965	0.0274	-0.0614	-0.1548	-0.8503	0.4734	-0.0941	0.277	-0.0472	0.0085	0.186	0.0096	0.2694	11.4243	19.6359	26.0586
6	3.6163	-2.2447	0.5155	2.9613	0.1608	3.0143	0.0379	0.2114	-0.11	-0.3194	-0.0072	0.0246	0.0569	-0.0328	0.0613	0.2931	-0.0027	0.0003	0.2195	-0.0164	0.1508	9.9408	7.2793	14.0392
7	2.0678	0.4838	0.4446	2.7476	-1.9773	3.1234	0.1861	-0.0933	0.1048	0.084	-0.2592	0.2042	-0.0908	-0.2218	0.022	0.2277	0.0028	0.0073	0.2099	-0.0203	0.1949	1.5029	14.1673	21.9201
8	3.831	-1.1289	0.0957	8.1657	0.8283	7.1536	-0.4414	0.0582	-0.7922	-0.7712	0.3489	-0.1722	0.7418	0.4195	0.038	0.3435	0.0355	0.0658	0.1858	-0.0076	0.2577	2.2056	4.2049	-11.5314
9	3.0595	0.8203	-0.428	3.4327	-3.5283	3.776	-0.0073	0.2193	-0.0608	-0.727	0.0616	1.2025	0.5272	-0.1712	-0.0585	0.2958	-0.0033	-0.025	0.1885	0.0075	0.337	-9.4823	19.0303	-11.3987
10	5.2099	-2.4786	1.2502	4.689	-0.9184	3.5892	-0.1088	0.5584	-0.2234	-1.1041	-0.0591	0.2546	0.5039	0.0811	0.0973	0.4875	-0.0183	0.0104	0.2273	-0.0079	0.1891	2.2792	20.6161	-17.2848
11	2.9563	2.5378	3.7916	3.6891	4.1916	5.4542	0.2233	0.8275	-0.0954	-0.3814	0.9018	-1.2364	0.5616	0.9662	-0.8411	0.4845	0.0479	0.1293	0.3673	-0.0478	0.4525	10.8098	19.7748	-14.234
12	1.6961	0.6542	0.1545	1.9246	-0.8408	3.7298	0.0435	-0.0361	0.1438	-0.0072	-0.0033	0.1175	-0.5125	-0.2244	-0.0655	0.2503	0.0179	-0.0208	0.1663	-0.0089	0.2437	-2.6419	26.1991	-2.8127
13	4.1282	2.6819	2.3115	1.9975	0.3817	7.4345	-0.0225	-0.5128	0.1472	0.2383	-0.1463	0.4163	0.4404	-0.3071	0.2245	0.2188	0.0594	0.0329	0.211	-0.0426	0.185	-4.84	14.6528	4.6267
14	4.0085	3.4753	2.3083	3.1028	1.7095	2.1808	0.3585	0.0375	-0.621	0.6164	0.1003	-0.2194	0.5638	-0.0308	-0.3287	0.4337	-0.0196	-0.0226	0.2037	0.0295	0.2591	0.2351	6.6886	1.7327
15	1.1264	-0.2008	0.1976	3.0325	1.0132	2.0871	0.0182	-0.0575	-0.0126	-0.3873	-0.0993	0.0452	-0.0908	0.2535	0.0696	0.3038	0.0021	0.0143	0.1966	0.0154	0.1961	7.0729	19.5302	-1.9301

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 13 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 14 through 20 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 21 through 31 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 32 through 49 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 50 through 73 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 74 through 93 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 94 through 126 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 13 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 14 through 31 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 32 through 43 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 44 through 49 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 50 through 73 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 74 through 82 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 83 through 93 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 94 through 126 )

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