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- PDB-2p71: Bombyx mori pheromone binding protein bound to iodohexadecane -

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Basic information

Entry
Database: PDB / ID: 2p71
TitleBombyx mori pheromone binding protein bound to iodohexadecane
Componentspheromone-binding protein
KeywordsATTRACTANT / alpha-helical / binding pocket / liganded
Function / homology
Function and homology information


response to pheromone / pheromone binding
Similarity search - Function
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
1-IODOHEXADECANE / Pheromone-binding protein
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.006 Å
AuthorsLautenschlager, C.L. / Clardy, J.
CitationJournal: Structure / Year: 2007
Title: Bombyx mori pheromone-binding protein binding nonpheromone ligands: implications for pheromone recognition.
Authors: Lautenschlager, C. / Leal, W.S. / Clardy, J.
History
DepositionMar 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pheromone-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2742
Polymers14,9221
Non-polymers3521
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.790, 83.790, 34.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein pheromone-binding protein / PBP


Mass: 14921.991 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Description: untagged / Gene: pheromone binding protein / Production host: Escherichia coli (E. coli) / References: UniProt: P34174
#2: Chemical ChemComp-IHD / 1-IODOHEXADECANE


Mass: 352.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H33I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 40.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, Tris, MgSO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.95 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.006→59.76 Å / Num. all: 13400 / Num. obs: 11314 / % possible obs: 92 % / Observed criterion σ(F): 2 / Biso Wilson estimate: 26 Å2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DQE

1dqe


Resolution: 2.006→59.76 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.889 / SU B: 4.656 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 392 4.9 %RANDOM
Rwork0.22 ---
all0.223 ---
obs0.223 8056 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.882 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2---0.68 Å20 Å2
3---1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.006→59.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 17 27 1082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0380.0211077
X-RAY DIFFRACTIONr_bond_other_d0.0030.02942
X-RAY DIFFRACTIONr_angle_refined_deg2.8151.9541444
X-RAY DIFFRACTIONr_angle_other_deg1.33432229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9435131
X-RAY DIFFRACTIONr_chiral_restr0.1810.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.021176
X-RAY DIFFRACTIONr_gen_planes_other0.0320.02190
X-RAY DIFFRACTIONr_nbd_refined0.2930.2290
X-RAY DIFFRACTIONr_nbd_other0.2560.21041
X-RAY DIFFRACTIONr_nbtor_other0.1050.2617
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.229
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.320.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.23
X-RAY DIFFRACTIONr_mcbond_it1.8631.5655
X-RAY DIFFRACTIONr_mcangle_it3.10921046
X-RAY DIFFRACTIONr_scbond_it4.3313422
X-RAY DIFFRACTIONr_scangle_it6.2284.5398
LS refinement shellResolution: 2.006→2.058 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.365 27
Rwork0.197 583
obs-610

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