PDB-3fiq: Odorant Binding Protein OBP1

ID or keywords:

Entry

Database: PDB / ID: 3fiq

Title

Odorant Binding Protein OBP1

Components

Odorant-binding protein 1F

Keywords

TRANSPORT PROTEIN /

lipocalin / oderant-binding protein

Function / homology

Function and homology information

odorant binding / response to stimulus /

small molecule binding / sensory perception of smell / extracellular region
Similarity search - Function

Biological species

Rattus norvegicus (Norway rat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.599 Å

Authors

White, S.A.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of rat odorant-binding protein OBP1 at 1.6 A resolution
Authors: White, S.A. / Briand, L. / Scott, D.J. / Borysik, A.J.

History

Deposition	Dec 12, 2008	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	May 19, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 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_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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Download

PDBx/mmCIF format	3fiq.cif.gz	200 KB	Display	PDBx/mmCIF format
PDB format	pdb3fiq.ent.gz	161.7 KB	Display	PDB format
PDBx/mmJSON format	3fiq.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/fi/3fiq ftp://data.pdbj.org/pub/pdb/validation_reports/fi/3fiq	HTTPS FTP

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Related structure data

Related structure data	1e5pS S: Starting model for refinement
Similar structure data	1beb-1 3qzu-2 4orr-d 3d2c-6 1i05-d 4orx-1 2poy-2 2qxu-2 2gj5-d 1z0d-1 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
Related items in Molecule of the Month	#193 - Jan 2016 Siderocalin similarity (5) #78 - Jun 2006 Luciferase similarity (1)

Deposited unit

A: Odorant-binding protein 1F

B: Odorant-binding protein 1F

hetero molecules

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

1

A: Odorant-binding protein 1F

hetero molecules

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

2

B: Odorant-binding protein 1F

hetero molecules

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

Unit cell

Length a, b, c (Å)	42.010, 62.070, 109.230
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Odorant-binding protein 1F / OBP1 / RCG36470 Mass: 18090.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Obp1f, obp-1F, rCG_36470 / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: Q9QYU9, UniProt: P08937*PLUS
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 475 / 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: 1.97 Å³/Da / Density % sol: 37.5 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% polyethylene glycol 5000, 100mM NaF, 5% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID14-2 / Wavelength: 0.934 Å

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 15, 2007

Radiation

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

Radiation wavelength

Wavelength: 0.934 Å / Relative weight: 1

Reflection

Resolution: 1.599→29.348 Å / Num. all: 38593 / Num. obs: 37976 / % possible obs: 98.4 % / Redundancy: 3.4 % / R_merge(I) obs: 0.046 / R_sym value: 0.046 / Net I/σ(I): 12.359

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.6-1.69	2.6	0.22	3.5	13633	5148	0.22	93
1.69-1.79	3.6	0.172	4.5	18666	5208	0.172	99.7
1.79-1.91	3.6	0.116	6.7	17868	4960	0.116	99.7
1.91-2.06	3.6	0.075	10.1	16367	4584	0.075	99.3
2.06-2.26	3.5	0.056	13.2	14879	4230	0.056	99.1
2.26-2.53	3.5	0.045	16.1	13397	3852	0.045	99.4
2.53-2.92	3.5	0.038	18.3	11833	3418	0.038	99
2.92-3.58	3.4	0.031	20.2	9944	2918	0.031	99
3.58-5.06	3.4	0.027	21.5	7914	2310	0.027	99.4
5.06-42.01	3.2	0.027	20.6	4310	1348	0.027	98.9

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Processing

Software

Name	Version	Classification
SCALA	3.2.25	data processing
PHENIX		refinement
PDB_EXTRACT	3.006	data extraction
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1e5p

1e5p

Resolution: 1.599→29.343 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.909 / Isotropic thermal model: TLS + ISOTROPIC / Cross valid method: THROUGHOUT / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.181	1895	5 %	random
R_work	0.141	-	-	-
all	-	37916	-	-
obs	-	37916	-	-

Solvent computation

B_sol: 54.043 Å² / k_sol: 0.391 e/Å³

Displacement parameters

B_iso max: 84.13 Å² / B_iso mean: 15.264 Å² / B_iso min: 3.95 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.808 Å²	-0 Å²	0 Å²
2-	-	-2.865 Å²	0 Å²
3-	-	-	3.672 Å²

Refinement step

Cycle: LAST / Resolution: 1.599→29.343 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4914	0	20	475	5409

Refine LS restraints

Refine-ID	Type	Dev ideal	Weight
X-RAY DIFFRACTION	f_angle_d	1.288	1
X-RAY DIFFRACTION	f_bond_d	0.015	1
X-RAY DIFFRACTION	f_chiral_restr	0.122	1
X-RAY DIFFRACTION	f_dihedral_angle_d	17.318	1
X-RAY DIFFRACTION	f_plane_restr	0.008	1
X-RAY DIFFRACTION	f_nbd_refined	3.76	1

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Total num. of bins used	% reflection obs (%)
1.599-1.603	0.215	156	X-RAY DIFFRACTION	134	29
1.603-1.607	0.2	269	X-RAY DIFFRACTION	134	51
1.607-1.611	0.205	363	X-RAY DIFFRACTION	134	64
1.611-1.615	0.196	380	X-RAY DIFFRACTION	134	70
1.615-1.62	0.201	385	X-RAY DIFFRACTION	134	74
1.62-1.624	0.192	459	X-RAY DIFFRACTION	134	80
1.624-1.628	0.168	446	X-RAY DIFFRACTION	134	82
1.628-1.632	0.191	443	X-RAY DIFFRACTION	134	82
1.632-1.637	0.191	449	X-RAY DIFFRACTION	134	87
1.637-1.641	0.194	440	X-RAY DIFFRACTION	134	84
1.641-1.645	0.189	465	X-RAY DIFFRACTION	134	85
1.645-1.65	0.184	464	X-RAY DIFFRACTION	134	87
1.65-1.654	0.177	525	X-RAY DIFFRACTION	134	88
1.654-1.659	0.173	490	X-RAY DIFFRACTION	134	89
1.659-1.664	0.176	471	X-RAY DIFFRACTION	134	91
1.664-1.668	0.17	506	X-RAY DIFFRACTION	134	90
1.668-1.673	0.178	560	X-RAY DIFFRACTION	134	95
1.673-1.678	0.165	514	X-RAY DIFFRACTION	134	95
1.678-1.683	0.17	484	X-RAY DIFFRACTION	134	94
1.683-1.688	0.171	492	X-RAY DIFFRACTION	134	94
1.688-1.692	0.164	478	X-RAY DIFFRACTION	134	91
1.692-1.698	0.168	533	X-RAY DIFFRACTION	134	92
1.698-1.703	0.152	499	X-RAY DIFFRACTION	134	92
1.703-1.708	0.174	485	X-RAY DIFFRACTION	134	95
1.708-1.713	0.157	532	X-RAY DIFFRACTION	134	96
1.713-1.718	0.167	543	X-RAY DIFFRACTION	134	93
1.718-1.724	0.175	496	X-RAY DIFFRACTION	134	94
1.724-1.729	0.162	503	X-RAY DIFFRACTION	134	95
1.729-1.735	0.174	522	X-RAY DIFFRACTION	134	94
1.735-1.74	0.17	536	X-RAY DIFFRACTION	134	94
1.74-1.746	0.143	524	X-RAY DIFFRACTION	134	95
1.746-1.751	0.145	503	X-RAY DIFFRACTION	134	97
1.751-1.757	0.162	502	X-RAY DIFFRACTION	134	96
1.757-1.763	0.147	526	X-RAY DIFFRACTION	134	94
1.763-1.769	0.142	511	X-RAY DIFFRACTION	134	95
1.769-1.775	0.15	511	X-RAY DIFFRACTION	134	96
1.775-1.781	0.142	503	X-RAY DIFFRACTION	134	93
1.781-1.787	0.163	503	X-RAY DIFFRACTION	134	92
1.787-1.793	0.144	544	X-RAY DIFFRACTION	134	95
1.793-1.8	0.151	508	X-RAY DIFFRACTION	134	94
1.8-1.806	0.137	481	X-RAY DIFFRACTION	134	94
1.806-1.813	0.132	536	X-RAY DIFFRACTION	134	93
1.813-1.819	0.16	544	X-RAY DIFFRACTION	134	96
1.819-1.826	0.14	524	X-RAY DIFFRACTION	134	94
1.826-1.833	0.147	502	X-RAY DIFFRACTION	134	95
1.833-1.84	0.14	509	X-RAY DIFFRACTION	134	99
1.84-1.847	0.137	497	X-RAY DIFFRACTION	134	93
1.847-1.854	0.127	524	X-RAY DIFFRACTION	134	95
1.854-1.861	0.144	500	X-RAY DIFFRACTION	134	93
1.861-1.868	0.147	544	X-RAY DIFFRACTION	134	93
1.868-1.876	0.147	510	X-RAY DIFFRACTION	134	95
1.876-1.883	0.141	486	X-RAY DIFFRACTION	134	95
1.883-1.891	0.155	525	X-RAY DIFFRACTION	134	93
1.891-1.899	0.131	498	X-RAY DIFFRACTION	134	93
1.899-1.907	0.139	521	X-RAY DIFFRACTION	134	92
1.907-1.915	0.138	505	X-RAY DIFFRACTION	134	93
1.915-1.923	0.133	503	X-RAY DIFFRACTION	134	90
1.923-1.932	0.138	497	X-RAY DIFFRACTION	134	95
1.932-1.94	0.122	517	X-RAY DIFFRACTION	134	95
1.94-1.949	0.146	498	X-RAY DIFFRACTION	134	96
1.949-1.958	0.139	515	X-RAY DIFFRACTION	134	95
1.958-1.967	0.138	515	X-RAY DIFFRACTION	134	93
1.967-1.976	0.13	499	X-RAY DIFFRACTION	134	93
1.976-1.985	0.141	552	X-RAY DIFFRACTION	134	95
1.985-1.995	0.117	496	X-RAY DIFFRACTION	134	93
1.995-2.005	0.13	504	X-RAY DIFFRACTION	134	93
2.005-2.015	0.132	510	X-RAY DIFFRACTION	134	93
2.015-2.025	0.132	510	X-RAY DIFFRACTION	134	94
2.025-2.035	0.127	523	X-RAY DIFFRACTION	134	95
2.035-2.046	0.126	489	X-RAY DIFFRACTION	134	94
2.046-2.056	0.137	520	X-RAY DIFFRACTION	134	96
2.056-2.067	0.128	533	X-RAY DIFFRACTION	134	96
2.067-2.079	0.126	495	X-RAY DIFFRACTION	134	92
2.079-2.09	0.136	535	X-RAY DIFFRACTION	134	94
2.09-2.102	0.124	512	X-RAY DIFFRACTION	134	95
2.102-2.114	0.126	446	X-RAY DIFFRACTION	134	92
2.114-2.126	0.119	542	X-RAY DIFFRACTION	134	91
2.126-2.139	0.127	509	X-RAY DIFFRACTION	134	92
2.139-2.151	0.128	447	X-RAY DIFFRACTION	134	91
2.151-2.165	0.117	536	X-RAY DIFFRACTION	134	94
2.165-2.178	0.119	504	X-RAY DIFFRACTION	134	94
2.178-2.192	0.123	511	X-RAY DIFFRACTION	134	91
2.192-2.206	0.125	516	X-RAY DIFFRACTION	134	91
2.206-2.221	0.113	511	X-RAY DIFFRACTION	134	94
2.221-2.236	0.129	467	X-RAY DIFFRACTION	134	93
2.236-2.251	0.121	516	X-RAY DIFFRACTION	134	93
2.251-2.267	0.128	514	X-RAY DIFFRACTION	134	94
2.267-2.283	0.13	526	X-RAY DIFFRACTION	134	92
2.283-2.3	0.134	478	X-RAY DIFFRACTION	134	91
2.3-2.318	0.128	502	X-RAY DIFFRACTION	134	92
2.318-2.335	0.134	511	X-RAY DIFFRACTION	134	90
2.335-2.354	0.114	481	X-RAY DIFFRACTION	134	93
2.354-2.373	0.129	522	X-RAY DIFFRACTION	134	93
2.373-2.392	0.128	488	X-RAY DIFFRACTION	134	96
2.392-2.413	0.122	540	X-RAY DIFFRACTION	134	94
2.413-2.434	0.131	489	X-RAY DIFFRACTION	134	93
2.434-2.455	0.116	498	X-RAY DIFFRACTION	134	92
2.455-2.478	0.132	528	X-RAY DIFFRACTION	134	93
2.478-2.501	0.127	508	X-RAY DIFFRACTION	134	93
2.501-2.526	0.131	453	X-RAY DIFFRACTION	134	91
2.526-2.551	0.127	537	X-RAY DIFFRACTION	134	92
2.551-2.577	0.132	488	X-RAY DIFFRACTION	134	90
2.577-2.604	0.131	513	X-RAY DIFFRACTION	134	92
2.604-2.633	0.142	483	X-RAY DIFFRACTION	134	93
2.633-2.663	0.133	527	X-RAY DIFFRACTION	134	94
2.663-2.694	0.13	499	X-RAY DIFFRACTION	134	93
2.694-2.727	0.13	489	X-RAY DIFFRACTION	134	92
2.727-2.761	0.123	535	X-RAY DIFFRACTION	134	95
2.761-2.798	0.134	508	X-RAY DIFFRACTION	134	92
2.798-2.836	0.134	469	X-RAY DIFFRACTION	134	91
2.836-2.877	0.137	524	X-RAY DIFFRACTION	134	93
2.877-2.92	0.136	489	X-RAY DIFFRACTION	134	93
2.92-2.965	0.145	501	X-RAY DIFFRACTION	134	91
2.965-3.014	0.128	532	X-RAY DIFFRACTION	134	94
3.014-3.066	0.132	480	X-RAY DIFFRACTION	134	92
3.066-3.121	0.13	511	X-RAY DIFFRACTION	134	91
3.121-3.181	0.124	491	X-RAY DIFFRACTION	134	93
3.181-3.246	0.119	520	X-RAY DIFFRACTION	134	94
3.246-3.316	0.123	496	X-RAY DIFFRACTION	134	94
3.316-3.394	0.116	514	X-RAY DIFFRACTION	134	92
3.394-3.478	0.119	516	X-RAY DIFFRACTION	134	94
3.478-3.572	0.113	512	X-RAY DIFFRACTION	134	94
3.572-3.677	0.118	486	X-RAY DIFFRACTION	134	91
3.677-3.796	0.115	519	X-RAY DIFFRACTION	134	94
3.796-3.931	0.128	509	X-RAY DIFFRACTION	134	95
3.931-4.088	0.126	507	X-RAY DIFFRACTION	134	94
4.088-4.273	0.109	511	X-RAY DIFFRACTION	134	94
4.273-4.498	0.111	517	X-RAY DIFFRACTION	134	95
4.498-4.779	0.116	521	X-RAY DIFFRACTION	134	95
4.779-5.146	0.139	517	X-RAY DIFFRACTION	134	95
5.146-5.66	0.159	509	X-RAY DIFFRACTION	134	94
5.66-6.472	0.206	500	X-RAY DIFFRACTION	134	93
6.472-8.125	0.214	528	X-RAY DIFFRACTION	134	94
8.125-29.348	0.19	502	X-RAY DIFFRACTION	134	93

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	4.6313	0.4546	2.7634	7.777	-1.2767	-1.1916	-0.0885	-0.3589	0.4021	1.062	-0.0823	-0.3563	-0.1061	-0.4018	0.1935	0.1912	-0.0038	-0.038	0.1386	-0.0295	0.1075	14.6939	4.4042	-33.5852
2	0.7309	-0.0599	-0.1031	0.7819	-0.2396	0.6845	0.0293	-0.0076	0.0226	-0.0429	-0.0211	0.0167	0.0359	0.0698	-0.0063	0.0642	0.0031	-0.0004	0.0544	-0.0072	0.0422	8.9876	-9.9364	-30.4642
3	0.6477	-0.1584	0.0744	0.2858	0.1936	0.5994	-0.013	-0.0088	0.0223	-0.0355	0.0056	-0.0073	0.025	-0.0375	0.0194	0.0736	0.0006	0.0052	0.0595	0.0072	0.0643	3.5636	-5.2679	-33.2096
4	-1.063	-0.1355	0.1476	1.1922	-0.0384	0.7022	0.0038	0.0047	0.0414	0.0112	0.0281	-0.0466	0.0062	0.0317	-0.0442	0.0471	0.0048	0.0019	0.0648	0.0019	0.035	9.0824	-6.6103	-25.5697
5	0.891	-0.0614	0.2782	0.8964	-0.7112	0.7992	0.0069	-0.1463	-0.0024	0.1168	-0.0334	-0.0506	-0.028	0.1719	0.0165	0.0703	-0.0019	-0.0063	0.0989	-0.0075	0.0439	14.2318	-11.4427	-19.6451
6	0.6977	-0.4634	-0.1897	1.1878	0.08	0.6185	0.0121	0.0425	0.0051	-0.0571	-0.0381	0.0052	0.0952	0.0232	0.0393	0.0813	0.005	-0.0096	0.0725	0.006	0.0326	-12.4732	5.197	3.9166
7	3.3506	-0.9638	0.9666	-8.6909	1.7441	2.6245	0.6323	-0.0626	-1.3214	0.6527	-0.1825	0.0301	0.5109	-0.171	-0.4156	0.4926	-0.1603	0.0536	0.1119	-0.072	0.5658	-21.4459	-12.5776	2.0126
8	0.4435	0.2818	-0.1984	0.5683	-0.1666	1.5429	-0.0288	-0.0777	-0.1043	-0.0008	-0.0477	-0.0873	0.1764	0.0793	0.0884	0.0736	0.0057	-0.0001	0.0703	0.0027	0.0432	-13.2791	5.6141	12.5693
9	0.7317	0.0026	0.284	0.9625	-0.4522	0.5229	0.0104	0.1085	-0.0228	-0.1012	-0.0955	0.0043	0.0737	0.1195	0.0655	0.0895	0.0261	0.0143	0.0914	0.0126	0.0524	-5.2196	2.1537	1.263
10	0.0202	0.2039	4.45	1.1428	-1.2375	1.4499	-0.1468	-0.053	-0.0528	0.576	0.0301	0.1445	0.0359	-0.5142	0.1798	0.3766	-0.0673	0.0164	0.2112	-0.0512	0.1567	-20.7699	-3.1164	-6.6003

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain A and resseq 20:26	A	20 - 26
2	X-RAY DIFFRACTION	2	chain A and resseq 27:63	A	27 - 63
3	X-RAY DIFFRACTION	3	chain A and resseq 64:108	A	64 - 108
4	X-RAY DIFFRACTION	4	chain A and resseq 109:139	A	109 - 139
5	X-RAY DIFFRACTION	5	chain A and resseq 140:173	A	140 - 173
6	X-RAY DIFFRACTION	6	chain B and resseq 17:73	B	17 - 73
7	X-RAY DIFFRACTION	7	chain B and resseq 74:78	B	74 - 78
8	X-RAY DIFFRACTION	8	chain B and resseq 79:95	B	79 - 95
9	X-RAY DIFFRACTION	9	chain B and resseq 96:167	B	96 - 167
10	X-RAY DIFFRACTION	10	chain B and resseq 168:173	B	168 - 173

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