PDB-7vw8: Helicoverpa armigera pheromone-binding protein PBP1 at pH 7.5

ID or keywords:

Entry

Database: PDB / ID: 7vw8

Title

Helicoverpa armigera pheromone-binding protein PBP1 at pH 7.5

Components

PBP1

Keywords

TRANSPORT PROTEIN / Ligand binding mechanism

Function / homology

Odorant/pheromone binding protein, Lepidoptera / Insect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / PBP1

Function and homology information

Biological species

Helicoverpa armigera (cotton bollworm)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.3 Å

Authors

Zheng, J. / Chen, Z.

Funding support

China, 1items

Citation

Journal: Int J Mol Sci / Year: 2022
Title: Structural Insights into the Ligand-Binding and -Releasing Mechanism of Helicoverpa armigera Pheromone-Binding Protein PBP1.
Authors: Zheng, J. / Yang, M. / Dong, K. / Zhang, J. / Wang, H. / Xie, M. / Wu, W. / Zhang, Y.J. / Chen, Z.

History

Deposition	Nov 9, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 2, 2022	Provider: repository / Type: Initial release
Revision 1.1	Mar 2, 2022	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.2	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7vw8.cif.gz	68 KB	Display	PDBx/mmCIF format
PDB format	pdb7vw8.ent.gz	47.4 KB	Display	PDB format
PDBx/mmJSON format	7vw8.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7vw8_validation.pdf.gz	423 KB	Display	wwPDB validaton report
Full document	7vw8_full_validation.pdf.gz	424.2 KB	Display
Data in XML	7vw8_validation.xml.gz	7.6 KB	Display
Data in CIF	7vw8_validation.cif.gz	9.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vw/7vw8 ftp://data.pdbj.org/pub/pdb/validation_reports/vw/7vw8	HTTPS FTP

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Related structure data

Related structure data	7vw9C 7vwaC 2fjyS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7vw9-d 1xfr-d 2bit-d 2pl9-1 4lzl-d 6vq5-2 2y77-d 3nv2-d 6xvs-1 7bgx-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

Deposited unit

A: PBP1

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, monomer

Unit cell

Length a, b, c (Å)	32.030, 32.604, 54.792
Angle α, β, γ (deg.)	90.000, 97.884, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	PBP1 Mass: 16384.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicoverpa armigera (cotton bollworm) / Gene: HaOG200775, B5X24_HaOG200775 / Production host: Escherichia coli (E. coli) / References: UniProt: F5ANH9
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.73 Å³/Da / Density % sol: 28.89 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: peg

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Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: 100K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 12, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.3→50 Å / Num. obs: 27772 / % possible obs: 93.1 % / Redundancy: 4.3 % / CC_1/2: 0.985 / R_merge(I) obs: 0.066 / Net I/σ(I): 17.7
Reflection shell	Resolution: 1.3→1.32 Å / R_merge(I) obs: 0.5 / Num. unique obs: 1306 / CC_1/2: 0.912

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
HKL-2000		data reduction
HKL-2000		data scaling
BALBES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2FJY

2fjy

Resolution: 1.3→20.866 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.939 / R_factor R_free error: 0.05 / SU B: 2.525 / SU ML: 0.046 / Data cutoff high absF: 2 / Data cutoff low absF: 2 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.08 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1976	1108	4.961 %	RANDOM
R_work	0.1787	21224	-	-
all	0.18	-	-	-
obs	0.1797	22332	80.328 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 20.223 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.156 Å²	-0 Å²	-1.412 Å²
2-	-	-1.523 Å²	-0 Å²
3-	-	-	1.993 Å²

Refinement step

Cycle: LAST / Resolution: 1.3→20.866 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1048	0	0	62	1110

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	1072
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	993
X-RAY DIFFRACTION	r_angle_refined_deg	1.378	1.634	1447
X-RAY DIFFRACTION	r_angle_other_deg	1.482	1.589	2308
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.632	5	134
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.934	26.122	49
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.704	15	195
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.835	15	1
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	139
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1208
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	218
X-RAY DIFFRACTION	r_nbd_refined	0.226	0.2	263
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.179	0.2	890
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	540
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	410
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.163	0.2	33
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.28	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.267	0.2	52
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.187	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	1.792	1.72	539
X-RAY DIFFRACTION	r_mcbond_other	1.736	1.717	538
X-RAY DIFFRACTION	r_mcangle_it	2.341	2.591	672
X-RAY DIFFRACTION	r_mcangle_other	2.349	2.594	673
X-RAY DIFFRACTION	r_scbond_it	2.183	2.101	533
X-RAY DIFFRACTION	r_scbond_other	2.183	2.101	533
X-RAY DIFFRACTION	r_scangle_it	2.566	3.004	775
X-RAY DIFFRACTION	r_scangle_other	2.564	3.007	776
X-RAY DIFFRACTION	r_lrange_it	2.869	21.526	1241
X-RAY DIFFRACTION	r_lrange_other	2.863	21.424	1235
X-RAY DIFFRACTION	r_rigid_bond_restr	3.227	3	2065

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 (%)
1.3-1.334	0.249	43	0.223	736	X-RAY DIFFRACTION	38.2238
1.334-1.371	0.299	52	0.233	978	X-RAY DIFFRACTION	52.6585
1.371-1.41	0.323	56	0.182	1143	X-RAY DIFFRACTION	61.4242
1.41-1.454	0.193	60	0.166	1364	X-RAY DIFFRACTION	76.0684
1.454-1.501	0.212	84	0.155	1558	X-RAY DIFFRACTION	90.6181
1.501-1.554	0.158	98	0.15	1650	X-RAY DIFFRACTION	98.4234
1.554-1.613	0.185	97	0.139	1613	X-RAY DIFFRACTION	99.7666
1.613-1.678	0.148	72	0.138	1554	X-RAY DIFFRACTION	100
1.678-1.753	0.207	75	0.135	1498	X-RAY DIFFRACTION	100
1.753-1.838	0.146	81	0.144	1432	X-RAY DIFFRACTION	99.868
1.838-1.938	0.174	69	0.151	1353	X-RAY DIFFRACTION	99.7195
1.938-2.055	0.196	60	0.154	1269	X-RAY DIFFRACTION	96.7249
2.055-2.197	0.159	63	0.158	1118	X-RAY DIFFRACTION	92.2656
2.197-2.372	0.2	52	0.159	998	X-RAY DIFFRACTION	88.7574
2.372-2.598	0.179	45	0.176	878	X-RAY DIFFRACTION	83.5294
2.598-2.904	0.221	28	0.212	742	X-RAY DIFFRACTION	76.4648
2.904-3.351	0.226	30	0.226	538	X-RAY DIFFRACTION	64.9886
3.351-4.099	0.231	25	0.23	349	X-RAY DIFFRACTION	48.7614
4.099-5.778	0.293	11	0.26	295	X-RAY DIFFRACTION	52.0408
5.778-10	0.334	7	0.312	158	X-RAY DIFFRACTION	47.0085

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	0.0656	0.2505	-0.1299	2.1856	-0.7705	0.3189	-0.0249	0.0136	0.0088	-0.0687	0.0419	0.0288	0.0431	-0.0221	-0.017	0.0202	-0.0029	0.0063	0.0285	0.0002	0.0106	18.5704	19.4108	26.2747
2	0.3526	0.399	-0.6808	0.667	-0.762	1.3147	-0.0143	0.0217	0.0078	-0.002	0.0287	0.0299	0.0285	-0.0402	-0.0144	0.0145	-0.001	0.0113	0.0266	0.0001	0.0129	14.3293	7.8622	39.0041
3	0.2304	-0.141	-0.1012	2.7024	0.3201	0.2958	-0.0382	-0.0424	0.0296	0.025	0.0179	-0.0415	0.0175	-0.029	0.0203	0.0212	0.003	0.0031	0.0362	-0.007	0.0173	10.8259	6.3309	49.5272
4	0.0558	0.0165	0.1335	0.0049	0.0393	0.3203	-0.0022	-0.0023	0.0017	-0.0001	0.0003	0.001	-0.0079	-0.0082	0.0019	0.0165	0.0012	0.0134	0.027	0.0001	0.0112	9.8619	20.2792	40.4301
5	0.4241	-0.3666	-0.2415	0.3273	0.1618	0.352	-0.0054	0.0009	0.0061	0.0051	0.0019	-0.0057	0.0087	-0.0041	0.0035	0.0144	-0.0012	0.0114	0.0253	0.0002	0.0093	18.5368	12.0128	45.9872
6	1.2957	0.3964	-1.0434	2.0681	-0.3786	3.6133	0.023	-0.0411	-0.0173	0.0501	-0.031	-0.0505	-0.0493	0.0304	0.0079	0.0125	-0.0003	0.0067	0.0274	0.0018	0.007	30.1223	11.4612	47.7809
7	0.003	0.0064	-0.003	0.1465	0.0576	0.1849	0.0008	0.0033	-0.0002	-0.0046	-0.0011	-0.0038	-0.0024	0.0025	0.0003	0.0152	0	0.0114	0.0251	0.0003	0.0089	29.8621	16.8186	33.7379
8	0.2911	0.5773	-1.0778	1.3305	-2.0242	4.5591	0.019	-0.0175	0.0095	0.0402	0.0026	-0.0172	-0.0658	0.0315	-0.0216	0.014	-0.0006	0.0068	0.0292	-0.0067	0.0147	28.1087	23.3209	53.3115
9	0.0402	-0.0615	0.1043	0.2695	-0.2812	0.3571	-0.0024	-0.0011	-0.0013	0.017	0.0039	-0.001	-0.0185	-0.0061	-0.0015	0.0158	0.0004	0.0104	0.0256	-0	0.0085	20.4926	22.6192	44.7351
10	0.3717	0.0348	-0.3313	0.2451	-0.0817	0.3167	-0.0032	0.0127	0.0168	0.015	0.0086	0.0006	0.0136	-0.0049	-0.0053	0.0199	0.0015	0.0117	0.0256	0.0012	0.0084	18.6434	26.2781	30.5595
11	0.1159	-0.0132	-0.0163	0.0531	-0.0349	0.0677	-0.0011	-0.0129	0.0067	-0.0016	-0.0013	-0.0013	0.0026	-0.0177	0.0024	0.0204	-0.001	0.013	0.0348	-0.0036	0.0089	20.4151	17.09	36.9089

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	24 - 35
2	X-RAY DIFFRACTION	2	ALL	A	36 - 47
3	X-RAY DIFFRACTION	3	ALL	A	48 - 55
4	X-RAY DIFFRACTION	4	ALL	A	56 - 69
5	X-RAY DIFFRACTION	5	ALL	A	70 - 88
6	X-RAY DIFFRACTION	6	ALL	A	89 - 95
7	X-RAY DIFFRACTION	7	ALL	A	96 - 125
8	X-RAY DIFFRACTION	8	ALL	A	126 - 133
9	X-RAY DIFFRACTION	9	ALL	A	134 - 151
10	X-RAY DIFFRACTION	10	ALL	A	152 - 158
11	X-RAY DIFFRACTION	11	ALL	A	201 - 262

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