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- PDB-2fjy: Crystal Structure of B-form Bombyx mori Pheromone Binding Protein -

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Basic information

Entry
Database: PDB / ID: 2fjy
TitleCrystal Structure of B-form Bombyx mori Pheromone Binding Protein
ComponentsPheromone-binding protein
KeywordsTRANSPORT PROTEIN / alpha helical
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
Pheromone-binding protein
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLautenschlager, C. / Leal, W.S. / Clardy, J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2005
Title: Coil-to-helix transition and ligand release of Bombyx mori pheromone-binding protein.
Authors: Lautenschlager, C. / Leal, W.S. / Clardy, J.
History
DepositionJan 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pheromone-binding protein
B: Pheromone-binding protein


Theoretical massNumber of molelcules
Total (without water)31,8062
Polymers31,8062
Non-polymers00
Water1,71195
1
A: Pheromone-binding protein


Theoretical massNumber of molelcules
Total (without water)15,9031
Polymers15,9031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pheromone-binding protein


Theoretical massNumber of molelcules
Total (without water)15,9031
Polymers15,9031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.240, 70.790, 75.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a monomer. There are 2 biological units in the asymmetric unit (chains A & B), which are separated by a translation of 0.497 along the b-axis and 0.051 along the c-axis.

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Components

#1: Protein Pheromone-binding protein / PBP


Mass: 15903.138 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: PBP / Production host: Escherichia coli (E. coli) / References: UniProt: P34174
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: NaF, PEG 3350, pH 7.5, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.95 Å
DetectorDetector: CCD / Date: Jun 5, 2002
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2→43 Å / Num. obs: 12094 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1GM0

1gm0


Resolution: 2.3→43 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.617 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.514 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27 605 5 %RANDOM
Rwork0.22 ---
all0.222 13439 --
obs0.22 12080 89.89 %-
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: 26.569 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--2.59 Å20 Å2
3----2.36 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 0 95 2261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0480.0212212
X-RAY DIFFRACTIONr_bond_other_d0.0040.021922
X-RAY DIFFRACTIONr_angle_refined_deg2.5331.9462985
X-RAY DIFFRACTIONr_angle_other_deg1.13334528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5625276
X-RAY DIFFRACTIONr_chiral_restr0.1740.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022458
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02394
X-RAY DIFFRACTIONr_nbd_refined0.2310.2583
X-RAY DIFFRACTIONr_nbd_other0.250.22147
X-RAY DIFFRACTIONr_nbtor_other0.0980.21227
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3140.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3650.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.27
X-RAY DIFFRACTIONr_mcbond_it2.3241.51378
X-RAY DIFFRACTIONr_mcangle_it4.41422201
X-RAY DIFFRACTIONr_scbond_it5.1533834
X-RAY DIFFRACTIONr_scangle_it8.054.5784
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.334 42
Rwork0.23 790
obs-832

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