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

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Basic information

Entry
Database: PDB / ID: 4inx
TitleStructure of Pheromone-binding protein 1 in complex with (Z,Z)-11,13- hexadecadienol
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-dien-1-ol / Pheromone-binding protein 1
Similarity search - Component
Biological speciesAmyelois transitella (butterflies/moths)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.853 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 1.1Oct 30, 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)16,1062
Polymers15,8671
Non-polymers2381
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.532, 57.532, 93.501
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-1EX / (11Z,13Z)-hexadeca-11,13-dien-1-ol


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


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.82 Å3/Da / Density % sol: 56.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / 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: 1.2 Å
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: 1.2 Å / Relative weight: 1
ReflectionRedundancy: 2.8 % / Av σ(I) over netI: 28.42 / Number: 41040 / Rmerge(I) obs: 0.04 / Χ2: 1.28 / D res high: 1.85 Å / D res low: 50 Å / Num. obs: 14800 / % possible obs: 98.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.995097.710.0261.1212.8
3.163.9999.510.0321.4922.8
2.763.1699.710.0381.3512.8
2.512.7699.410.0421.3432.8
2.332.5199.310.0471.3812.8
2.192.3399.310.0531.342.8
2.082.1999.310.0541.1512.7
1.992.0898.910.0711.2662.8
1.921.9998.310.0851.1412.8
1.851.9291.810.1131.1512.7
ReflectionResolution: 1.85→50 Å / Num. all: 15052 / Num. obs: 14800 / % possible obs: 98.3 % / Observed criterion σ(I): 28.4 / Redundancy: 2.8 % / Rmerge(I) obs: 0.04 / Χ2: 1.276 / Net I/σ(I): 16.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.922.70.11313711.151191.8
1.92-1.992.80.08514741.141198.3
1.99-2.082.80.07114681.266198.9
2.08-2.192.70.05414901.151199.3
2.19-2.332.80.05314851.34199.3
2.33-2.512.80.04715071.381199.3
2.51-2.762.80.04214861.343199.4
2.76-3.162.80.03814981.351199.7
3.16-3.992.80.03215111.492199.5
3.99-502.80.02615101.121197.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.853→34.1 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 2.427 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2138 605 4.1 %RANDOM
Rwork0.168 ---
all0.168 14023 --
obs0.1701 14628 98.98 %-
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 max: 44.7 Å2 / Biso mean: 13.0968 Å2 / Biso min: 2.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.09 Å20 Å2
2--0.17 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.853→34.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 17 161 1281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221148
X-RAY DIFFRACTIONr_angle_refined_deg1.8721.9771540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5255141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.16826.15452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06315219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.895153
X-RAY DIFFRACTIONr_chiral_restr0.4090.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.021842
X-RAY DIFFRACTIONr_mcbond_it1.3011.5700
X-RAY DIFFRACTIONr_mcangle_it2.25921125
X-RAY DIFFRACTIONr_scbond_it4.1543448
X-RAY DIFFRACTIONr_scangle_it6.3784.5414
LS refinement shellResolution: 1.853→1.901 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 43 -
Rwork0.157 1001 -
all-1044 -
obs--97.57 %

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