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- PDB-1dqe: BOMBYX MORI PHEROMONE BINDING PROTEIN -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1dqe
TitleBOMBYX MORI PHEROMONE BINDING PROTEIN
ComponentsPHEROMONE-BINDING PROTEIN
KeywordsTRANSPORT PROTEIN / HELICAL BUNDLE
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
HEXADECA-10,12-DIEN-1-OL / Pheromone-binding protein
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsSandler, B.H. / Nikonova, L. / Leal, W.S. / Clardy, J.
CitationJournal: Chem.Biol. / Year: 2000
Title: Sexual attraction in the silkworm moth: structure of the pheromone-binding-protein-bombykol complex.
Authors: Sandler, B.H. / Nikonova, L. / Leal, W.S. / Clardy, J.
History
DepositionJan 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHEROMONE-BINDING PROTEIN
B: PHEROMONE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2324
Polymers30,7552
Non-polymers4772
Water3,657203
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.180, 53.180, 191.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PHEROMONE-BINDING PROTEIN / PBP


Mass: 15377.497 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Escherichia coli (E. coli) / References: UniProt: P34174
#2: Chemical ChemComp-BOM / HEXADECA-10,12-DIEN-1-OL / BOMBYKOL


Mass: 238.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H30O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: PEG20000, Tris, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.65 Methanol1drop
220 mg/mlprotein1drop
350 %(w/v)PEG200001reservoir
4100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9134
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9134 Å / Relative weight: 1
ReflectionResolution: 1.8→32.4 Å / Num. all: 26572 / Num. obs: 26466 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 19.743 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 9.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.264 / Num. unique all: 3770 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 135291

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementResolution: 1.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1330 5 %random
Rwork0.21 ---
all-26572 --
obs-26466 99.6 %-
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 34 203 2377
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.012
X-RAY DIFFRACTIONp_bond_d2.4
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.218 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.4
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg22.1
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.9

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