PDB-4f7f: Structure of Anopheles gambiae odorant binding protein 20

ID or keywords:

Entry

Database: PDB / ID: 4f7f

Title

Structure of Anopheles gambiae odorant binding protein 20

Components

AGAP005208-PA

Keywords

ODORANT-BINDING PROTEIN / insect / odoroant binding protein / transport / secreted

Function / homology

Function and homology information

dibutyl phthalate binding / olfactory behavior / odorant binding / sensory perception of smell / extracellular region
Similarity search - Function

Biological species

Anopheles gambiae (African malaria mosquito)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Jones, D.N. / Ziemba, B.P.

Citation

Journal: Protein Sci. / Year: 2013
Title: A novel mechanism of ligand binding and release in the odorant binding protein 20 from the malaria mosquito Anopheles gambiae.
Authors: Ziemba, B.P. / Murphy, E.J. / Edlin, H.T. / Jones, D.N.

History

Deposition	May 16, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 17, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 7, 2012	Group: Database references
Revision 1.2	Dec 26, 2012	Group: Database references
Revision 1.3	Nov 15, 2017	Group: Refinement description / Structure summary / Category: audit_author / software / Item: _audit_author.name / _software.name
Revision 1.4	Sep 13, 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	4f7f.cif.gz	205.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4f7f.ent.gz	168.1 KB	Display	PDB format
PDBx/mmJSON format	4f7f.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4f7f_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	4f7f_full_validation.pdf.gz	1 MB	Display
Data in XML	4f7f_validation.xml.gz	24 KB	Display
Data in CIF	4f7f_validation.cif.gz	33.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f7/4f7f ftp://data.pdbj.org/pub/pdb/validation_reports/f7/4f7f	HTTPS FTP

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Related structure data

Related structure data	3v2lC 3vb1C 3qdi PDB Unreleased entryS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3t6k-d 3jwp-d 6onp-d 6h1y-d 5ida-4 2yj7-d 2ijx-2 5t9p-6 6dkq-d 6mlv-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) 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

3v2lC

3vb1C

3qdi
PDB Unreleased entryS

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#222 - Jun 2018 Proteins and Nanoparticles similarity (1)

Deposited unit

A: AGAP005208-PA

B: AGAP005208-PA

C: AGAP005208-PA

D: AGAP005208-PA

hetero molecules

55 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: AGAP005208-PA

B: AGAP005208-PA

hetero molecules

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

2

C: AGAP005208-PA

D: AGAP005208-PA

hetero molecules

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

3

A: AGAP005208-PA

hetero molecules

D: AGAP005208-PA

hetero molecules

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

4

B: AGAP005208-PA

C: AGAP005208-PA

hetero molecules

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

Unit cell

Length a, b, c (Å)	130.794, 36.374, 96.154
Angle α, β, γ (deg.)	90.00, 91.22, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-266- HOH

#1: Protein	AGAP005208-PA Mass: 13450.953 Da / Num. of mol.: 4 / Fragment: OBP20 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anopheles gambiae (African malaria mosquito) Gene: OBP20, AgaP_AGAP005208 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Q9J3
#2: Chemical	ChemComp-2PE / NONAETHYLENE GLYCOL Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₃₈O₁₀ / Comment: precipitant*YM
#3: Chemical	ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE Mass: 266.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₆
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.13 Å³/Da / Density % sol: 42.12 %
Crystal grow	Temperature: 276 K / Method: vapor diffusion, hanging drop / pH: 5.57 Details: 0.2 M potassium sodium tartrate, 0.1 M sodium citrate, 1.9 M ammonium sulfate, pH 5.57, VAPOR DIFFUSION, HANGING DROP, temperature 276K

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Data collection

Diffraction	Mean temperature: 95 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
Detector	Type: NOIR-1 / Detector: CCD / Date: Feb 4, 2010
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.66→34 Å / Num. all: 54923 / Num. obs: 48493 / % possible obs: 88.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / R_merge(I) obs: 0.062 / Net I/σ(I): 8.5
Reflection shell	Resolution: 1.66→1.72 Å / R_merge(I) obs: 0.38 / Mean I/σ(I) obs: 2.3 / % possible all: 94

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Processing

Software

Name	Version	Classification
JBluIce-EPICS		data collection
Blu-Ice	ICE	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
d*TREK		data reduction
d*TREK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QDI

3qdi
PDB Unreleased entry

Resolution: 1.8→24.033 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.48 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2508	1859	5.04 %	Random
R_work	0.1954	-	-	-
all	0.1982	36854	-	-
obs	0.1982	36854	86.59 %	-

Solvent computation

Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 37.545 Å² / k_sol: 0.336 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.3819 Å²	0 Å²	-2.8249 Å²
2-	-	2.1674 Å²	0 Å²
3-	-	-	-0.7855 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→24.033 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3636	0	70	302	4008

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	3798
X-RAY DIFFRACTION	f_angle_d	1.276	5067
X-RAY DIFFRACTION	f_dihedral_angle_d	14.542	1509
X-RAY DIFFRACTION	f_chiral_restr	0.076	582
X-RAY DIFFRACTION	f_plane_restr	0.006	649

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 (%)
1.8-1.8487	0.4098	149	0.323	2831	X-RAY DIFFRACTION	93
1.8487-1.903	0.3717	153	0.3058	2842	X-RAY DIFFRACTION	92
1.903-1.9644	0.3078	140	0.2165	2777	X-RAY DIFFRACTION	91
1.9644-2.0346	0.2771	148	0.2166	2746	X-RAY DIFFRACTION	88
2.0346-2.116	0.2571	135	0.1945	2655	X-RAY DIFFRACTION	86
2.116-2.2123	0.2732	130	0.1976	2640	X-RAY DIFFRACTION	86
2.2123-2.3288	0.2859	143	0.2053	2630	X-RAY DIFFRACTION	84
2.3288-2.4746	0.3121	149	0.2031	2478	X-RAY DIFFRACTION	81
2.4746-2.6654	0.3101	125	0.2097	2470	X-RAY DIFFRACTION	79
2.6654-2.9332	0.2531	127	0.2066	2458	X-RAY DIFFRACTION	79
2.9332-3.3567	0.2787	136	0.2037	2507	X-RAY DIFFRACTION	80
3.3567-4.2254	0.2034	149	0.1728	2777	X-RAY DIFFRACTION	88
4.2254-24.0353	0.1874	175	0.1628	3184	X-RAY DIFFRACTION	98

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	4.2733	-5.1001	-0.1701	8.0155	0.0281	2.7602	0.0484	-0.5691	-0.6807	0.2512	-0.0704	0.7623	-0.015	-0.2567	0.1173	0.2183	-0.0467	0.0028	0.189	0.0104	0.1603	66.8921	43.1238	74.7057
2	5.7005	-1.0374	-0.8919	4.6403	-1.8164	2.5505	0.0045	-0.3065	0.4035	0.2908	-0.0129	0.3786	-0.4583	-0.0675	0.0273	0.1824	0.0244	-0.0286	0.1485	-0.043	0.2731	79.2903	50.5114	69.2118
3	2.9623	2.1095	0.5441	4.0856	0.9485	4.5339	-0.1503	-0.1267	-0.7065	-0.0402	0.0316	-0.0627	0.2253	-0.2998	0.0875	0.118	0.0006	-0.0001	0.0965	0.0013	0.1766	76.8216	40.3073	66.9163
4	4.8345	1.6557	-0.2151	8.8636	-4.2258	6.711	-0.3484	0.1177	-0.5079	-0.2072	0.2081	-0.4148	0.4602	0.1047	0.0157	0.1287	0.0238	-0.0184	0.2323	0.0067	0.3232	69.5845	34.5234	59.8882
5	2.3217	-0.8042	0.8621	5.3216	1.7847	2.3723	-0.1881	-0.2115	0.1783	0.3478	-0.1432	0.5983	0.1387	-0.4413	0.3307	0.1984	-0.0106	-0.0106	0.2431	-0.0552	0.1797	59.9459	44.4155	59.7015
6	4.6294	-0.2144	2.0658	0.8028	-1.1176	3.1098	-0.1485	0.7265	0.0882	-0.0575	0.0135	-0.2188	-0.0493	0.4216	0.0993	0.1413	-0.0303	-0.0072	0.2241	-0.0164	0.1232	75.2678	43.139	55.7639
7	7.6384	-3.0495	-0.0127	8.6778	-6.679	7.4092	-0.4002	-0.6943	0.5579	0.1333	-0.2	-0.4189	-0.5667	-0.0426	0.5024	0.2563	0.0567	-0.0637	0.171	-0.0519	0.1846	66.917	51.6249	63.9205
8	6.3651	2.7347	1.5584	3.931	1.1016	3.3032	-0.138	0.2709	0.0585	0.0888	-0.0967	-0.8412	-0.359	0.409	0.1387	0.1979	-0.0249	-0.0411	0.1641	0.0572	0.2917	62.4799	25.1607	68.727
9	5.0036	0.8249	-0.1329	3.9043	-0.2088	2.5478	0.0284	-0.2767	0.4425	0.0592	0.0178	-0.2168	-0.8676	0.4102	-0.0582	0.263	-0.0582	-0.0063	0.1438	-0.0043	0.1998	49.7462	32.5662	74.0973
10	8.9023	-4.325	0.5485	4.7715	-0.7812	3.3935	-0.107	-0.2303	-0.0918	0.0394	0.0711	-0.2125	0.1318	0.1372	0.057	0.1566	-0.0227	0.0051	0.1236	-0.0004	0.136	52.324	22.1466	76.0796
11	6.7714	3.3562	-3.4527	5.3576	-2.8357	6.1207	-0.609	0.0904	-0.4451	-0.1829	0.1522	-0.4532	0.6776	0.3663	0.2577	0.1999	0.0314	-0.0061	0.157	0.0557	0.2708	59.4629	16.3829	83.2372
12	1.6674	-0.095	1.955	3.2578	-0.875	2.471	-0.2752	0.6618	0.6009	-0.0483	-0.3356	-0.8522	-0.5462	0.6943	-0.0383	0.2248	-0.0741	-0.2103	0.3648	0.1886	0.3953	68.2646	26.7561	84.9371
13	3.9478	0.0996	2.0656	1.3739	0.601	4.0894	-0.1557	-0.4105	0.2633	0.3371	-0.1344	-0.1257	-0.2002	-0.3199	0.2662	0.202	0.022	-0.0526	0.1908	-0.0022	0.1513	52.827	24.393	87.2415
14	0.3448	0.0816	0.5902	0.0192	0.1394	1.0125	-0.666	0.2094	0.0631	0.0151	-0.034	-0.4378	-0.5707	0.3353	-0.1469	0.4604	-0.1505	-0.1194	0.2393	0.0319	0.3998	61.0311	33.2846	81.2429
15	1.311	0.0151	-0.0256	7.2724	-2.0405	1.5455	-0.2826	-0.1692	0.0954	0.1079	0.2998	-0.4722	-0.3403	0.1212	-0.0226	0.1744	-0.019	-0.0246	0.1522	-0.0509	0.2079	40.5876	2.2626	70.413
16	4.9202	-1.1229	0.5905	5.1417	-0.0687	6.1293	-0.2948	0.1729	0.3212	-0.109	0.2901	-0.1974	-0.2942	-0.3757	0.0046	0.2162	-0.0449	0.0338	0.1637	-0.0179	0.1364	35.127	10.9298	62.4393
17	5.6507	0.8159	-2.0766	4.432	0.5247	2.46	-0.1169	-0.2515	0.2076	-0.0459	0.9099	-0.894	-0.9151	0.6493	-0.3405	0.5144	0.0182	0.1509	0.3675	-0.1025	0.29	45.5001	1.9308	54.4348
18	2.4245	-0.4504	0.1307	1.1691	0.2693	1.8313	0.094	0.2262	-0.1278	-0.4367	0.0469	-0.2662	-0.2057	0.3084	-0.0117	0.2298	-0.0245	0.0487	0.1531	-0.0329	0.149	36.1156	-1.5665	55.4918
19	2.1535	-2.4906	-1.4403	8.4782	5.9426	5.0773	0.1106	-0.052	0.134	-0.309	-0.2095	0.0432	-0.3956	-0.3386	0.0556	0.1145	0.0008	-0.0224	0.1216	0.0284	0.1197	21.6848	2.2861	73.6882
20	7.3712	0.0228	2.4348	5.1516	-1.7354	5.9348	0.1794	0.3625	-0.0111	-0.6121	-0.0746	0.0804	-0.0856	0.2778	-0.0663	0.2446	-0.0085	0.035	0.0843	-0.0138	0.1074	29.5305	12.6101	78.5208
21	5.5579	2.194	0.4968	4.9013	0.889	4.1582	-0.0275	-0.3606	0.3496	-0.1852	-0.1184	0.3329	-0.0194	-0.4404	0.1212	0.1325	0.012	0.0042	0.1724	0.0038	0.0986	24.2984	9.2662	85.8509
22	3.7543	-1.0756	-4.8227	3.5309	0.9051	7.7082	0.1883	0.0932	0.2736	-0.3141	0.1794	0.0701	0.2884	-0.6789	-0.3255	0.2214	-0.1122	0.0288	0.3598	0.0256	0.1933	18.386	-1.3914	89.5023
23	1.1669	0.1392	-0.0475	2.8653	0.7039	1.6375	0.0948	-0.1356	-0.0929	0.0943	-0.0687	-0.0147	0.2437	-0.342	-0.0253	0.1631	-0.0474	-0.0259	0.1796	0.0344	0.1037	27.7275	-3.174	88.0649

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 2:21)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 22:39)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 40:52)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 53:62)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 63:88)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 89:113)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 114:120)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 2:21)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 22:39)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 40:52)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 53:62)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 63:89)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 90:112)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 113:120)
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 2:21)
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 22:52)
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 53:62)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 63:120)
19	X-RAY DIFFRACTION	19	chain 'D' and (resseq 2:21)
20	X-RAY DIFFRACTION	20	chain 'D' and (resseq 22:33)
21	X-RAY DIFFRACTION	21	chain 'D' and (resseq 34:52)
22	X-RAY DIFFRACTION	22	chain 'D' and (resseq 53:62)
23	X-RAY DIFFRACTION	23	chain 'D' and (resseq 63:120)

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