PDB-3s0g: Apis mellifera OBP 14 double mutant Gln44Cys, His97Cys

ID or keywords:

Entry

Database: PDB / ID: 3s0g

Title

Apis mellifera OBP 14 double mutant Gln44Cys, His97Cys

Components

OBP14

Keywords

TRANSPORT PROTEIN / all helical protein / unknown odorant molecules / antennae

Function / homology

Function and homology information

odorant binding / extracellular region
Similarity search - Function

Biological species

Apis mellifera (honey bee)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIR / Resolution: 1.85 Å

Authors

Spinelli, S. / Lagarde, A. / Iovinella, I. / Tegoni, M. / Pelosi, P. / Cambillau, C.

Citation

Journal: Insect Biochem.Mol.Biol. / Year: 2012
Title: Crystal structure of Apis mellifera OBP14, a C-minus odorant-binding protein, and its complexes with odorant molecules.
Authors: Spinelli, S. / Lagarde, A. / Iovinella, I. / Legrand, P. / Tegoni, M. / Pelosi, P. / Cambillau, C.

History

Deposition	May 13, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 30, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jan 11, 2012	Group: Database references
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references / 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3s0g.cif.gz	98.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3s0g.ent.gz	77.8 KB	Display	PDB format
PDBx/mmJSON format	3s0g.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/s0/3s0g ftp://data.pdbj.org/pub/pdb/validation_reports/s0/3s0g	HTTPS FTP

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Related structure data

Related structure data	3rzsC 3s0aC 3s0bC 3s0dC 3s0eC 3s0fSC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3s0f-1 3s0d-d 3rzs-d 3s0a-d 3s0b-d 3s0f-2 3h9x-4 3s0e-d 2qgv-9 2byc-2 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: OBP14

B: OBP14

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

1

A: OBP14

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

2

B: OBP14

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

Unit cell

Length a, b, c (Å)	63.790, 72.990, 42.040
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	B-178- HOH
2	1	B-179- HOH

#1: Protein	OBP14 / odorant binding protein 14 Mass: 13493.621 Da / Num. of mol.: 2 / Fragment: UNP residues 18-135 / Mutation: Q44C,H97C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Apis mellifera (honey bee) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q1W640
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H₂O
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: 1.81 Å³/Da / Density % sol: 32.17 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.6 M sodium phosphate monobasic, 1.6 M potassium phosphate dibasic, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9786
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 9, 2011 / Details: mirrors
Radiation	Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 1.85→36.6 Å / Num. all: 17250 / Num. obs: 17250 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / B_iso Wilson estimate: 19.64 Å² / R_merge(I) obs: 0.074 / Net I/σ(I): 16.1
Reflection shell	Resolution: 1.85→1.95 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.47 / Mean I/σ(I) obs: 4 / Num. unique all: 2481 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
MOLREP		phasing
BUSTER	2.9.2	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MIR
Starting model: PDB ENTRY 3S0F

3s0f

Resolution: 1.85→35.1 Å / Cor.coef. F_o:F_c: 0.9239 / Cor.coef. F_o:F_c free: 0.9116 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2278	871	5.06 %	RANDOM
R_work	0.2207	-	-	-
all	0.2211	17214	-	-
obs	0.2211	17214	-	-

Displacement parameters

B_iso max: 76.25 Å² / B_iso mean: 21.47 Å² / B_iso min: 4.96 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.2807 Å²	0 Å²	0 Å²
2-	-	-0.9704 Å²	0 Å²
3-	-	-	2.2511 Å²

Refine analyze

Luzzati coordinate error obs: 0.26 Å

Refinement step

Cycle: LAST / Resolution: 1.85→35.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1872	0	0	183	2055

Refine LS restraints

Refine-ID	Type	Number	Restraint function	Weight	Dev ideal
X-RAY DIFFRACTION	t_dihedral_angle_d	720	SINUSOIDAL	2
X-RAY DIFFRACTION	t_trig_c_planes	68	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes	250	HARMONIC	5
X-RAY DIFFRACTION	t_it	1892	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_chiral_improper_torsion	264	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact	2587	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_bond_d	1892	HARMONIC	2	0.01
X-RAY DIFFRACTION	t_angle_deg	2546	HARMONIC	2	1.37
X-RAY DIFFRACTION	t_omega_torsion				2.38
X-RAY DIFFRACTION	t_other_torsion				22.02

LS refinement shell

Resolution: 1.85→1.96 Å / Total num. of bins used: 9

	R_factor	Num. reflection	% reflection
R_free	0.2636	136	4.95 %
R_work	0.2463	2610	-
all	0.2471	2746	-

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	0	0.0053	0.0098	0.0088	0.0266	0.0009	0.0003	-0.0007	0.0009	0.0003	0.0002	-0.0006	-0.0018	0.0016	-0.0004	-0.002	0.0073	-0.0015	-0.0046	-0.0005	-0.0082	48.2129	31.1048	16.3419
2	0.0108	0.0087	0.0213	0.003	0.0028	0.0004	0.0004	-0.0001	-0.0013	0	0.0003	0.0003	0.0001	-0.0011	-0.0007	-0.0023	0.0017	-0.0047	-0.003	-0.0066	-0.0033	45.8647	18.0647	13.5093
3	0.0003	-0.0193	0.0212	0.0091	0.0185	0.0003	0.0001	0.0011	-0.0012	-0.0016	-0.0002	0.0005	0.0019	-0.0001	0.0001	0.0021	-0.0052	-0.0031	-0.0057	-0.0008	-0.0004	44.4657	10.367	18.7524
4	0.0198	0.0305	0.0487	0.0162	0.0075	0.0549	0.0003	-0.0003	-0.0008	-0.0005	0.0002	0.0001	0.001	0.0007	-0.0004	0.0031	0.0038	-0.0014	-0.0022	0.0011	0.0002	50.5498	11.7703	26.3741
5	0.0032	0.0084	0.0232	0.0196	0.0323	0.0164	-0.0003	-0.0007	-0.0008	-0.0012	0.0007	-0.001	-0.0015	-0.0003	-0.0003	-0.0023	0.0083	-0.0057	-0.0067	-0.0099	0.0015	52.6382	8.8531	17.461
6	0.0002	0.0081	0.0227	0.0173	0.0108	0.008	-0.0001	0.0001	-0.0001	0.0002	-0.0012	0.0007	0.0005	0.0007	0.0013	-0.002	-0.0005	0.0003	0.0008	-0.0028	-0.0044	59.1904	18.8511	12.8542
7	0	-0.027	0.0011	0	0.0177	0	0.0002	0.0009	-0.0026	-0.0004	-0.0001	-0.0019	0.0007	0.0018	-0.0001	-0.0065	-0.003	0.0006	-0.0029	0.0014	-0.0048	65.6402	21.7315	16.3246
8	0	0.0153	0.0122	0.0026	0.0213	0	-0.0001	0	0.0002	-0.0022	-0.0006	0.0001	-0.0003	-0.0001	0.0006	-0.0047	-0.0021	0.0004	-0.0068	-0.0023	-0.0011	59.105	31.4313	23.7378
9	0.0356	0.0109	-0.0317	0.0143	-0.0032	0	0	0.0001	-0.0013	-0.0008	-0.0004	-0.0008	0.0004	-0.0011	0.0004	-0.0051	-0.001	0.0056	0.0023	0.0025	0.0082	65.7902	24.4452	27.1709
10	0.0272	-0.058	-0.0229	0.0508	0.0249	0.0247	-0.0001	0.0012	-0.0009	-0.0005	-0.0009	-0.0001	0.0013	-0.0013	0.001	-0.0007	0.007	-0.0035	0.0003	-0.0055	0.0051	65.0694	9.0547	20.6671
11	0.0418	-0.0135	0.0432	0.0169	-0.0009	0	0.0004	-0.0004	-0.0002	0.0005	-0.0008	-0.0005	0.0003	0.0005	0.0004	-0.0054	0.0015	-0.0084	0.006	-0.0014	-0.0002	58.5346	15.8034	25.6099
12	0.0192	-0.0124	-0.0207	0.0184	-0.025	0.0349	0	0.0008	-0.0006	-0.0007	-0.0013	0.0003	-0.0008	-0.0007	0.0014	-0.0014	0.0019	0.004	0.004	-0.013	0.0019	49.1679	25.7167	26.7609
13	0	-0.0119	0.0106	0.0127	0.0079	0.025	0.0001	0.0011	0.0011	-0.0001	0.0001	-0.0011	-0.0026	0.0015	-0.0002	-0.0009	0.0018	0.0025	0.0005	0.0003	-0.0077	72.7978	53.0028	37.1261
14	0.0001	-0.003	0.0181	0.0054	0.0003	0.0157	0.0002	0.0004	0.0007	0.0003	0.0006	0.0011	-0.0007	0.0003	-0.0008	-0.0011	0.0019	-0.0043	0.0031	-0.0021	-0.0043	70.3371	39.8284	34.5823
15	0	0.0006	-0.0007	0.0062	-0.0255	0.0084	0.0001	0.0026	-0.0021	-0.0011	0.0001	-0.0002	-0.0003	0.0002	-0.0002	0.0024	-0.0026	-0.0059	-0.0079	-0.0046	-0.0052	68.6446	31.9379	40.4122
16	0.0279	0.0262	0.0333	0.0084	0.0001	0.0395	0.0006	-0.0004	-0.001	0.0004	0.0003	-0.0007	-0.0004	0.0003	-0.0009	0.0039	0.0081	-0.0007	-0.0055	-0.0001	0.0005	74.7049	34.0284	47.8603
17	0.0179	0.0216	0.0169	0.0095	-0.0066	0	-0.0004	0.0028	-0.0004	-0.0003	0.0001	0.0001	-0.0002	0.0007	0.0003	0.0002	0.0095	-0.005	-0.0048	-0.0081	-0.0002	76.9567	30.7455	38.9973
18	0.0103	-0.0043	0.0264	0.0003	-0.0187	0.0083	0	0.0002	-0.0008	-0.0001	-0.0004	-0.0007	0.0005	0.0003	0.0004	-0.004	0.008	-0.0044	0.0048	0.0051	-0.0011	83.6119	40.2846	34.0691
19	0	-0.008	0.0054	0	0.0076	0	0.0002	0.0003	-0.0003	0.0002	-0.0001	-0.0003	-0.0001	0.0005	-0.0002	-0.0034	-0.0021	-0.0012	-0.0012	0.0006	-0.0034	90.204	43.2985	37.7095
20	0	0.0308	-0.0058	0.0044	-0.0222	0.0023	0	0.0013	0.0003	-0.0014	-0.0007	0.0001	-0.0007	-0.0001	0.0007	-0.0037	-0.0068	-0.002	-0.0011	-0.001	-0.0039	83.7007	53.6556	44.6823
21	0.0193	-0.0125	-0.0144	0.0107	-0.0071	0	0.0001	0.0005	-0.0016	0	0	-0.0009	0.0003	0.0003	0	-0.0046	-0.0015	0.0037	0.0048	0.0005	0.0029	90.2465	46.412	48.4754
22	0.0087	-0.0029	-0.0104	0.0085	-0.0023	0.0135	0	0.0002	-0.0009	-0.0007	0.0002	-0.0001	0.0008	-0.0008	-0.0002	-0.0015	0.0008	-0.0018	0.001	-0.0018	0.0012	89.294	30.7286	42.3267
23	0	-0.0371	0.0302	0.0028	0.0059	0.0087	0.0003	0.0008	-0.0001	0.0003	0.0002	-0.0002	-0.0001	0.0006	-0.0005	-0.0039	0.0021	-0.0112	0.002	-0.0068	-0.0082	82.8022	37.6974	46.993
24	0.0089	-0.0473	-0.0147	0	-0.0489	0.0482	0.0006	0.002	-0.0014	-0.0013	-0.0012	0.0005	-0.0015	0.0009	0.0007	0.0024	-0.0004	-0.0047	-0.0003	-0.0062	-0.0075	73.7006	47.8392	47.6783

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{A\|1 - A\|10}	A	1 - 10
2	X-RAY DIFFRACTION	2	{A\|11 - A\|19}	A	11 - 19
3	X-RAY DIFFRACTION	3	{A\|20 - A\|29}	A	20 - 29
4	X-RAY DIFFRACTION	4	{A\|30 - A\|39}	A	30 - 39
5	X-RAY DIFFRACTION	5	{A\|40 - A\|49}	A	40 - 49
6	X-RAY DIFFRACTION	6	{A\|50 - A\|59}	A	50 - 59
7	X-RAY DIFFRACTION	7	{A\|60 - A\|69}	A	60 - 69
8	X-RAY DIFFRACTION	8	{A\|70 - A\|79}	A	70 - 79
9	X-RAY DIFFRACTION	9	{A\|80 - A\|89}	A	80 - 89
10	X-RAY DIFFRACTION	10	{A\|90 - A\|99}	A	90 - 99
11	X-RAY DIFFRACTION	11	{A\|100 - A\|109}	A	100 - 109
12	X-RAY DIFFRACTION	12	{A\|110 - A\|119}	A	110 - 119
13	X-RAY DIFFRACTION	13	{B\|1 - B\|10}	B	1 - 10
14	X-RAY DIFFRACTION	14	{B\|11 - B\|19}	B	11 - 19
15	X-RAY DIFFRACTION	15	{B\|20 - B\|29}	B	20 - 29
16	X-RAY DIFFRACTION	16	{B\|30 - B\|39}	B	30 - 39
17	X-RAY DIFFRACTION	17	{B\|40 - B\|49}	B	40 - 49
18	X-RAY DIFFRACTION	18	{B\|50 - B\|59}	B	50 - 59
19	X-RAY DIFFRACTION	19	{B\|60 - B\|69}	B	60 - 69
20	X-RAY DIFFRACTION	20	{B\|70 - B\|79}	B	70 - 79
21	X-RAY DIFFRACTION	21	{B\|80 - B\|89}	B	80 - 89
22	X-RAY DIFFRACTION	22	{B\|90 - B\|99}	B	90 - 99
23	X-RAY DIFFRACTION	23	{B\|100 - B\|109}	B	100 - 109
24	X-RAY DIFFRACTION	24	{B\|110 - B\|119}	B	110 - 119

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