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- PDB-4inw: Structure of Pheromone-binding protein 1 in complex with (11Z,13Z... -

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Basic information

Entry
Database: PDB / ID: 4inw
TitleStructure of Pheromone-binding protein 1 in complex with (11Z,13Z)-hexadecadienal
ComponentsPheromone-binding protein 1
Keywordspheromone-binding protein / Amyelois transitella / pheromone / navel orangeworm moth / AtraPBP1 / pH-dependent binding
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
(11Z,13Z)-hexadeca-11,13-dienal / Pheromone-binding protein 1
Similarity search - Component
Biological speciesAmyelois transitella (butterflies/moths)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.14 Å
Authorsdi Luccio, E. / Wilson, D.K.
CitationJournal: Plos One / Year: 2013
Title: Crystallographic Observation of pH-Induced Conformational Changes in the Amyelois transitella Pheromone-Binding Protein AtraPBP1.
Authors: di Luccio, E. / Ishida, Y. / Leal, W.S. / Wilson, D.K.
History
DepositionJan 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1042
Polymers15,8671
Non-polymers2361
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.455, 57.455, 93.268
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Pheromone-binding protein 1


Mass: 15867.321 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amyelois transitella (butterflies/moths)
Production host: Escherichia coli (E. coli) / References: UniProt: D0E9M1
#2: Chemical ChemComp-1EY / (11Z,13Z)-hexadeca-11,13-dienal


Mass: 236.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H28O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
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: 2.8 Å3/Da / Density % sol: 56.08 %
Crystal growTemperature: 295 K / pH: 6.5
Details: Purified AtraPBP1 was crystallized at room temperature by the hanging drop vapor diffusion method. Drops composed of 1ul protein solution (30 mg/ml) and 1ul of the precipitant solution were ...Details: Purified AtraPBP1 was crystallized at room temperature by the hanging drop vapor diffusion method. Drops composed of 1ul protein solution (30 mg/ml) and 1ul of the precipitant solution were suspended over a reservoir containing the precipitant solution (1.6 M sodium citrate pH 6.5). Crystals used in data collection were transferred into Paratone-N oil and flash-cooled in a stream of liquid nitrogen at 110 K, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.14→28.72 Å / % possible obs: 97.2 % / Observed criterion σ(I): 29.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.7 Å28.73 Å
Translation1.7 Å28.73 Å

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Processing

Software
NameVersionClassificationNB
PHASER1.3.1phasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.14→28.72 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 1.384 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.183 2326 4 %RANDOM
Rwork0.16 ---
obs0.161 57779 93.9 %-
all-55453 --
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: 17.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å2-0.57 Å20 Å2
2---1.13 Å20 Å2
3---1.7 Å2
Refinement stepCycle: LAST / Resolution: 1.14→28.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 17 179 1299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221173
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.9771578
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0745148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78126.07851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6715225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.136153
X-RAY DIFFRACTIONr_chiral_restr0.2870.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.021862
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.4771.5720
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.58121161
X-RAY DIFFRACTIONr_scbond_it6.3193453
X-RAY DIFFRACTIONr_scangle_it8.4814.5415
X-RAY DIFFRACTIONr_rigid_bond_restr2.13411173
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.14→1.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 136 -
Rwork0.24 3368 -
obs--84.33 %

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