PDB-8c6g: CRYSTAL STRUCTURE OF ODORANT BINDING PROTEIN 4 FROM ANOPHELES GAM...

ID or keywords:

Entry

Database: PDB / ID: 8c6g

Title

CRYSTAL STRUCTURE OF ODORANT BINDING PROTEIN 4 FROM ANOPHELES GAMBIAE (AGAMOBP4) AT PH 6.5

Components

AGAP010489-PA

Keywords

TRANSPORT PROTEIN / Odorant Binding Protein (OBP) / mosquito / olfaction

Function / homology

Function and homology information

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

Biological species

Anopheles gambiae (African malaria mosquito)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Tsitsanou, K.E. / Drakou, C.E. / Zographos, S.E.

Funding support

Greece, 2items

Citation

Journal: To Be Published
Title: Influence of pH on indole-dependent heterodimeric interactions between Anopheles gambiae odorant-binding proteins OBP1 and OBP4.
Authors: Mam, B. / Tsitsanou, K.E. / Liggri, P.G.V. / Saitta, F. / Stamati, E.C.V. / Mahita, J. / Leonis, G. / Drakou, C.E. / Papadopoulos, M. / Arnaud, P. / Offmann, B. / Fessas, D. / Sowdhamini, R. / Zographos, S.E.

History

Deposition	Jan 11, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 5, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 7, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8c6g.cif.gz	117.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8c6g.ent.gz	91.7 KB	Display	PDB format
PDBx/mmJSON format	8c6g.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/c6/8c6g ftp://data.pdbj.org/pub/pdb/validation_reports/c6/8c6g	HTTPS FTP

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Related structure data

Related structure data	3b7aS 8c68 8c6e S: Starting model for refinement
Similar structure data	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: AGAP010489-PA

B: AGAP010489-PA

hetero molecules

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

1

A: AGAP010489-PA

hetero molecules

defined by author
Evidence: gel filtration
14.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: AGAP010489-PA

hetero molecules

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

Unit cell

Length a, b, c (Å)	60.355, 57.030, 67.340
Angle α, β, γ (deg.)	90.00, 100.21, 90.00
Int Tables number	5
Space group name H-M	I121

#1: Protein	AGAP010489-PA / Odorant binding protein / Odorant-binding protein AgamOBP4 / Odorant-binding protein antennal 4 Mass: 14048.541 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anopheles gambiae (African malaria mosquito) Gene: OBP-4, 1275228, AgamOBP4, OBP4, AgaP_AGAP010489, agCG48601 Plasmid: PET-22B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMIB(DE3) / References: UniProt: Q8T6R7
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.03 Å³/Da / Density % sol: 39.4 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6 M TRI-SODIUM CITRATE, PH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03796 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 13, 2009 / Details: MULTILAYER MIRROR
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03796 Å / Relative weight: 1
Reflection	Resolution: 2.05→48.73 Å / Num. obs: 14115 / % possible obs: 99.3 % / Redundancy: 6.4 % / CC_1/2: 0.997 / R_merge(I) obs: 0.096 / R_pim(I) all: 0.041 / R_rim(I) all: 0.104 / Net I/σ(I): 12.5
Reflection shell	Resolution: 2.05→2.16 Å / Redundancy: 5.9 % / R_merge(I) obs: 0.474 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2046 / CC_1/2: 0.881 / R_pim(I) all: 0.209 / R_rim(I) all: 0.521 / % possible all: 98.4

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
SCALA		data scaling
MOSFLM		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B7A

3b7a

Resolution: 2.05→48.73 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.936 / SU B: 10.83 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.229	708	5 %	RANDOM
R_work	0.193	-	-	-
obs	0.195	14099	99 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 32.18 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.76 Å²	0 Å²	-0.62 Å²
2-	-	-2.09 Å²	0 Å²
3-	-	-	0.11 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→48.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1931	0	10	76	2017

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	2035
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.441	1.986	2739
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.572	5	259
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.71	25.789	76
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.208	15	403
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.613	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	293
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	1498
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.434	1.5	1291
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.729	2	2089
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.6	3	744
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.352	4.5	650
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.05→2.1 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.355	59	-
R_work	0.24	969	-
obs	-	-	97.9 %

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	5.4789	5.6092	-7.5831	12.4385	-6.5177	10.7286	-0.1783	0.0362	-0.0239	0.1237	0.1117	0.0621	0.3107	-0.0466	0.0666	0.1579	-0.0019	0.0233	0.1292	-0.0181	0.1548	-13.4235	-31.9314	10.4161
2	14.1498	-1.7675	-6.116	22.2554	-4.4714	29.0725	-0.3566	-0.3265	-0.7487	0.0377	0.1507	-0.3353	0.4228	0.4732	0.2059	0.0684	-0.013	0.0273	0.1526	-0.0328	0.0673	-8.0355	-24.9049	2.4467
3	2.5874	0.2461	-2.1002	0.8267	1.2598	6.2013	-0.0088	-0.0303	0.0315	0.0684	-0.0073	-0.0575	0.1801	0.0474	0.0161	0.0642	-0.0086	-0.011	0.0613	0.0004	0.0651	-5.5432	-15.4047	7.6264
4	7.5216	4.5176	-0.6419	18.5438	1.3159	6.2504	-0.1679	0.3362	0.252	-0.2997	0.2919	0.6726	-0.1106	-0.1744	-0.124	0.0539	0.0242	0.0048	0.1123	0.0326	0.0741	-11.9011	-13.6818	1.8072
5	2.2091	1.5729	2.4345	22.6322	-12.044	11.604	-0.323	0.2535	0.012	-0.7605	0.5401	0.1539	0.1189	-0.1944	-0.2171	0.256	-0.0232	-0.0214	0.6245	0.0098	0.445	-26.1078	-19.3927	4.5386
6	1.1981	-1.1643	-0.7328	17.9793	-2.6406	1.3879	0.0189	0.0995	0.0641	0.0841	0.0141	0.3838	0.1539	-0.2067	-0.0329	0.1584	-0.0245	0.0334	0.2244	-0.0072	0.1949	-23.7118	-17.9518	15.3273
7	4.4166	0.0885	-0.2443	4.5327	-1.5108	6.4595	-0.0327	0.0541	-0.0048	0.0808	0.0656	0.0601	0.0631	-0.1388	-0.0328	0.0163	-0.009	0.0325	0.0976	-0.0169	0.1269	-16.1638	-12.4022	11.1627
8	30.0926	2.2302	2.2346	8.655	-22.7846	62.2213	-0.3937	1.3573	-0.77	-0.2752	0.4171	-0.1246	0.6173	-0.9328	-0.0234	0.4933	-0.0862	0.03	0.3287	-0.1056	0.5311	-21.5995	-46.9654	4.1771
9	4.457	0.4143	0.8106	21.7133	-13.1249	10.9147	-0.0398	-0.6643	0.0038	0.4066	0.0554	0.2616	0.0655	-0.3113	-0.0156	0.3	0.028	-0.0296	0.3568	-0.101	0.1893	-22.2801	-34.8731	-3.0212
10	3.3126	0.0335	-0.0788	2.3431	0.6798	3.1085	-0.0505	-0.1103	0.3062	-0.0229	0.0317	0.0655	-0.1159	-0.1568	0.0188	0.137	-0.0071	-0.0278	0.1195	-0.0048	0.1034	-21.0548	-35.9001	-15.3847
11	4.1762	0.3674	-2.4872	8.1717	-0.7824	6.862	0.1777	-0.1385	-0.1999	0.0901	0.0631	-0.6139	0.1534	0.2055	-0.2408	0.2761	-0.0042	-0.1567	0.3145	-0.0625	0.2811	-4.6351	-36.8765	-6.1338
12	14.2876	17.3868	-2.6579	35.6619	-1.8837	6.9575	-0.368	-1.0288	-0.0565	1.0103	-0.1789	0.9353	-0.3728	-0.2821	0.547	0.6509	0.1441	0.0418	0.4808	0.0466	0.2821	-12.2602	-48.9925	0.6671
13	1.6126	-0.7118	0.333	10.0569	-5.9921	6.5716	0.0487	-0.0762	-0.0277	0.1671	-0.1546	-0.4377	0.2895	0.3532	0.1059	0.1686	0.007	-0.0241	0.1776	-0.0218	0.2499	-5.5189	-44.5631	-14.3296
14	11.1688	3.0428	-4.2843	1.9856	-2.4277	5.6319	0.0109	-0.1168	0.45	-0.0911	-0.0239	-0.2864	-0.0052	0.042	0.013	0.0744	0.0034	-0.0026	0.0679	-0.0091	0.2234	-11.0176	-37.8673	-17.1947
15	0.4417	3.1595	0.187	23.9707	2.1531	0.579	-0.0018	0.0193	0.0971	0.6122	-0.231	1.1445	0.2098	-0.243	0.2328	0.2768	-0.0025	-0.0099	0.3451	-0.0291	0.2972	-16.9146	-48.1944	-12.3079

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 12
2	X-RAY DIFFRACTION	2	A	13 - 17
3	X-RAY DIFFRACTION	3	A	18 - 40
4	X-RAY DIFFRACTION	4	A	41 - 56
5	X-RAY DIFFRACTION	5	A	57 - 77
6	X-RAY DIFFRACTION	6	A	78 - 99
7	X-RAY DIFFRACTION	7	A	100 - 125
8	X-RAY DIFFRACTION	8	B	2 - 6
9	X-RAY DIFFRACTION	9	B	7 - 21
10	X-RAY DIFFRACTION	10	B	22 - 53
11	X-RAY DIFFRACTION	11	B	54 - 72
12	X-RAY DIFFRACTION	12	B	73 - 83
13	X-RAY DIFFRACTION	13	B	84 - 102
14	X-RAY DIFFRACTION	14	B	103 - 112
15	X-RAY DIFFRACTION	15	B	113 - 125

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