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- PDB-7vwa: Helicoverpa armigera pheromone-binding protein PBP1 with Z-9-hexa... -

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Basic information

Entry
Database: PDB / ID: 7vwa
TitleHelicoverpa armigera pheromone-binding protein PBP1 with Z-9-hexadecenal
ComponentsPBP1
KeywordsTRANSPORT PROTEIN / Helicoverpa armigera / Pheromone binding protein / Ligand binding mechanism
Function / homology
Function and homology information


Odorant/pheromone binding protein, Lepidoptera / Pheromone/general odorant binding protein domain / Insect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(Z)-hexadec-9-enal / PBP1
Similarity search - Component
Biological speciesHelicoverpa armigera (cotton bollworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZheng, J. / Chen, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31872713 China
CitationJournal: 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
DepositionNov 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.4Mar 12, 2025Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.content_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PBP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6232
Polymers16,3851
Non-polymers2381
Water72140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7130 Å2
Unit cell
Length a, b, c (Å)32.907, 33.356, 56.044
Angle α, β, γ (deg.)90.00, 98.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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: Chemical ChemComp-81K / (Z)-hexadec-9-enal


Mass: 238.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: peg

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 7259 / % possible obs: 98.2 % / Redundancy: 4.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.057 / Net I/σ(I): 31.1
Reflection shellResolution: 2.09→2.13 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.302 / Num. unique obs: 277 / CC1/2: 0.953 / % possible all: 81

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VW9

7vw9


Resolution: 2.1→32.54 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 14.286 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23592 394 5.6 %RANDOM
Rwork0.19863 ---
obs0.20066 6682 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.795 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-1.63 Å2
2--0.63 Å20 Å2
3----0.31 Å2
Refinement stepCycle: 1 / Resolution: 2.1→32.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1059 0 17 40 1116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131099
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171034
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.6471478
X-RAY DIFFRACTIONr_angle_other_deg1.2971.6332404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0045137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.28726.04248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.90315193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.807151
X-RAY DIFFRACTIONr_chiral_restr0.0620.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021226
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02222
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1733.098551
X-RAY DIFFRACTIONr_mcbond_other0.1733.097550
X-RAY DIFFRACTIONr_mcangle_it0.2974.644687
X-RAY DIFFRACTIONr_mcangle_other0.2974.645688
X-RAY DIFFRACTIONr_scbond_it0.1523.122548
X-RAY DIFFRACTIONr_scbond_other0.1523.122548
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.2514.671792
X-RAY DIFFRACTIONr_long_range_B_refined0.88937.1161228
X-RAY DIFFRACTIONr_long_range_B_other0.85237.0691224
X-RAY DIFFRACTIONr_rigid_bond_restr0.68132133
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 19 -
Rwork0.242 432 -
obs--87.23 %

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