PDB-5ngh: Structure of Odorant Binding Protein 3 from Giant Panda (Ailuropo...

ID or keywords:

Entry

Database: PDB / ID: 5ngh

Title

Structure of Odorant Binding Protein 3 from Giant Panda (Ailuropoda melanoleuca)

Components

Odorant Binding Protein 3

Keywords

PROTEIN BINDING / Odorant Binding Protein Giant Panda Ailuropoda melanoleuca

Function / homology

Function and homology information

small molecule binding / extracellular region
Similarity search - Function

Biological species

Ailuropoda melanoleuca (giant panda)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Cambillau, C. / Spinelli, S. / Pelosi, P.

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Reverse chemical ecology: Olfactory proteins from the giant panda and their interactions with putative pheromones and bamboo volatiles.
Authors: Zhu, J. / Arena, S. / Spinelli, S. / Liu, D. / Zhang, G. / Wei, R. / Cambillau, C. / Scaloni, A. / Wang, G. / Pelosi, P.

History

Deposition	Mar 17, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 1, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2017	Group: Database references / Category: citation Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Nov 22, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Feb 28, 2018	Group: Structure summary / Category: audit_author / entity / Item: _audit_author.name / _entity.pdbx_description
Revision 1.4	Jan 17, 2024	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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ngh.cif.gz	74 KB	Display	PDBx/mmCIF format
PDB format	pdb5ngh.ent.gz	55 KB	Display	PDB format
PDBx/mmJSON format	5ngh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ngh_validation.pdf.gz	301.1 KB	Display	wwPDB validaton report
Full document	5ngh_full_validation.pdf.gz	305.6 KB	Display
Data in XML	5ngh_validation.xml.gz	9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ng/5ngh ftp://data.pdbj.org/pub/pdb/validation_reports/ng/5ngh	HTTPS FTP

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Related structure data

Related structure data	3kffS S: Starting model for refinement
Similar structure data	3zq3-1 6nre-d 3kff-d 5x7y-1 6y76-1 4wfv-d 1bso-d 4lzu-d 5x7y-3 4ib8-d 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 3

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	94.030, 94.030, 114.530
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein	Odorant Binding Protein 3 Mass: 19671.947 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ailuropoda melanoleuca (giant panda) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: G1LK14
#2: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.71 Å³/Da / Density % sol: 66.89 %
Crystal grow	Temperature: 273 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.2 M Ammonium Sulfate and 0.2M Potassium Nitrate at pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 21, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2.8→80 Å / Num. obs: 7821 / % possible obs: 99.9 % / Redundancy: 10.4 % / B_iso Wilson estimate: 104.93 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.2 / Net I/σ(I): 10.4
Reflection shell	Resolution: 2.8→2.97 Å / Redundancy: 10.3 % / Num. unique obs: 1218 / CC_1/2: 0.93 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
BUSTER	2.10.1	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3KFF

3kff

Resolution: 2.8→24.73 Å / Cor.coef. F_o:F_c: 0.8079 / Cor.coef. F_o:F_c free: 0.8051 / SU R Cruickshank DPI: 0.551 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.601 / SU R_free Blow DPI: 0.334 / SU R_free Cruickshank DPI: 0.329

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2877	389	5 %	RANDOM
R_work	0.2766	-	-	-
obs	0.2772	7784	99.65 %	-

Displacement parameters

B_iso mean: 93.18 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-27.4321 Å²	0 Å²	0 Å²
2-	-	-27.4321 Å²	0 Å²
3-	-	-	54.8641 Å²

Refine analyze

Luzzati coordinate error obs: 0.679 Å

Refinement step

Cycle: 1 / Resolution: 2.8→24.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1272	0	16	16	1304

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	1307	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.26	1770	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		459	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		41	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		188	HARMONIC	5
X-RAY DIFFRACTION	t_it		1307	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	2.93
X-RAY DIFFRACTION	t_other_torsion	25.38
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		172	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		1453	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.8→3.13 Å / Total num. of bins used: 5

	R_factor	Num. reflection	% reflection
R_free	0.4047	106	4.97 %
R_work	0.387	2025	-
all	0.3879	2131	-
obs	-	-	99.65 %

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	0.0053	-0.0018	0.0008	-0.001	-0.0015	0.0048	-0.0002	0.0002	-0.0002	0.0002	0	0.0004	0.0004	-0.0001	0.0002	0.0011	-0.0002	-0.0008	0.0009	0	0.0018	9.7879	-34.6054	-0.3782
2	-0.0102	0.0059	0.0031	0.0102	-0.0032	0.0069	0	-0.0001	0.0011	0.0002	0.0002	0.0005	0	-0.0004	-0.0002	0.0002	-0.0012	-0.0032	0.001	-0.0029	-0.0034	16.3228	-26.1755	-2.7427
3	0.018	-0.0104	0.0303	-0.018	-0.0176	0.059	0	0.0001	0.0042	-0.0011	-0.0005	0.0039	0.0004	0.0007	0.0005	0.0001	-0.0002	-0.0033	-0.0004	0.0005	-0.0015	22.7371	-32.2594	9.3009
4	0.003	-0.0042	-0.0016	0.0055	0.0135	0.003	-0.0001	0	-0.0004	0	0	0.0002	0.0002	-0.0002	0.0001	0.0007	0.0015	0.0001	0.0026	-0.0003	0.0013	37.9236	-44.6727	0.7468
5	-0.0058	0.0034	0.0094	0.0058	-0.0024	0.0037	0	-0.0008	-0.001	0.0007	-0.0001	-0.0003	0.0006	0.0004	0.0001	-0.0003	0.0017	-0.0016	0.0046	-0.0017	-0.001	39.4028	-41.6225	8.1855
6	0.003	-0.0017	-0.0107	-0.003	0.0009	0	0	0.0001	0.0002	0	0.0004	0	0.0006	0.0011	-0.0005	-0.0051	0.0004	0.003	0.0042	-0.0017	-0.0012	30.5388	-33.482	11.6028
7	0.0097	0.0127	-0.0068	0.0114	-0.0016	0	0	0.0005	0.0001	-0.0005	-0.0004	-0.0006	-0.0011	-0.0002	0.0003	0.0024	-0.0034	0.0028	0.0003	-0.0035	-0.0014	26.584	-19.9683	5.7041
8	0.0351	-0.0091	-0.0331	-0.0223	-0.0452	0.0124	-0.0005	0.0003	-0.0007	0.0008	0.0003	-0.0016	0.001	0.0006	0.0002	-0.0047	-0.0001	0.0023	0.0091	-0.0035	-0.0013	37.4766	-32.2044	16.0052
9	0.0008	0.0137	-0.0059	0.0156	-0.0323	0.0008	0.0011	0.0004	0.0007	-0.0016	-0.0009	0.0012	-0.0011	0.0002	-0.0003	0.0052	-0.0043	0.0027	-0.0008	-0.0011	-0.0031	29.7229	-22.3791	-2.6385
10	0.0515	-0.0297	-0.001	-0.0515	-0.0424	0	0	0.0003	-0.0004	-0.0005	0.0003	-0.002	-0.0007	0.0011	-0.0003	-0.0033	-0.0023	0.0008	0.0026	-0.001	-0.0004	35.6355	-27.0957	-0.3602
11	-0.0053	0.007	0.0035	0.0098	0.0101	0.0205	0.0001	-0.0006	0.0003	0.0001	0.0003	-0.0008	0.0004	0.0007	-0.0004	-0.0014	-0.0007	0.0017	0.0045	-0.0014	-0.0007	32.9041	-29.2038	-3.6623
12	0.0172	-0.01	0.0117	-0.0172	0.0013	0.0061	0.0002	-0.0008	0.001	0.0008	-0.0004	0.0007	-0.0001	-0.0003	0.0003	-0.001	-0.0001	-0.0045	0.0038	0.0001	-0.0023	17.2813	-31.9803	0.7856
13	0.0203	-0.0117	0.0087	-0.0203	0.0277	0.0125	0.0002	-0.0002	0.0003	-0.0002	0.0001	-0.001	0.0003	-0.0006	-0.0002	0.0018	-0.0017	-0.0011	0.0018	-0.0017	-0.0048	18.9646	-34.6472	4.3292
14	0.0442	-0.0255	0.0149	-0.0442	0.0466	0.0253	0.0005	-0.0001	-0.0003	-0.0011	-0.0003	-0.0047	0.0007	-0.0003	-0.0002	-0.0002	-0.0022	0.0003	0.0054	-0.0034	-0.0052	39.0641	-34.5156	-5.5514
15	-0.0624	0.0796	-0.0372	0.1127	0.0781	0	0.0003	0.0008	0.0008	-0.0002	-0.0011	0.0004	0.001	0.002	0.0008	0.0037	-0.0064	-0.0014	-0.0051	-0.0054	0.0017	28.2822	-37.8219	1.78
16	-0.0004	0.011	0.0193	0.0128	-0.0181	0.0064	0.0001	0.0004	0.0001	-0.0009	-0.0001	0.0004	0.0005	-0.0007	0	-0.003	-0.0047	0.0023	-0.003	0	0.0021	17.9637	-38.1242	12.5144
17	-0.0067	0.0264	0.0065	0.0328	0.0316	0.0114	0.0007	-0.0002	-0.0018	-0.0002	-0.0007	0.0002	0.001	-0.0004	0	0.0041	-0.0019	-0.0004	-0.0019	-0.0023	0.0008	18.0299	-45.0359	1.935
18	-0.0058	0.0074	-0.005	0.0104	0.0031	0	-0.0002	-0.0004	-0.0005	0.0004	0.0003	-0.0004	0.0009	0	0	0.0016	-0.0011	0.0001	-0.0029	0.0021	-0.0014	24.5046	-43.2854	-6.3373
19	-0.015	0.0215	0.0017	0.0586	-0.0121	0.0089	0.0001	-0.0001	0.0002	0	0	-0.0006	0.0002	0.0003	0	0.0063	-0.0016	0.0029	-0.0009	-0.002	-0.001	29.2808	-48.0663	2.39
20	-0.0166	0.0096	-0.004	0.0166	0.0019	0.0113	-0.0001	-0.0008	-0.0003	0.0003	0.0001	-0.0004	0.001	0.0005	0.0001	-0.0005	-0.0005	0.0003	0.0053	-0.0007	-0.0058	29.1311	-39.0741	18.2839

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{A\|3 - A\|7}
2	X-RAY DIFFRACTION	2	{A\|8 - A\|13}
3	X-RAY DIFFRACTION	3	{A\|14 - A\|26}
4	X-RAY DIFFRACTION	4	{A\|27 - A\|32}
5	X-RAY DIFFRACTION	5	{A\|33 - A\|39}
6	X-RAY DIFFRACTION	6	{A\|40 - A\|45}
7	X-RAY DIFFRACTION	7	{A\|46 - A\|56}
8	X-RAY DIFFRACTION	8	{A\|57 - A\|69}
9	X-RAY DIFFRACTION	9	{A\|70 - A\|80}
10	X-RAY DIFFRACTION	10	{A\|81 - A\|88}
11	X-RAY DIFFRACTION	11	{A\|89 - A\|93}
12	X-RAY DIFFRACTION	12	{A\|94 - A\|99}
13	X-RAY DIFFRACTION	13	{A\|100 - A\|105}
14	X-RAY DIFFRACTION	14	{A\|106 - A\|115}
15	X-RAY DIFFRACTION	15	{A\|116 - A\|123}
16	X-RAY DIFFRACTION	16	{A\|124 - A\|129}
17	X-RAY DIFFRACTION	17	{A\|130 - A\|138}
18	X-RAY DIFFRACTION	18	{A\|139 - A\|144}
19	X-RAY DIFFRACTION	19	{A\|145 - A\|153}
20	X-RAY DIFFRACTION	20	{A\|154 - A\|163}

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