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- PDB-3r72: Apis mellifera odorant binding protein 5 -

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Basic information

Entry
Database: PDB / ID: 3r72
TitleApis mellifera odorant binding protein 5
ComponentsOdorant binding protein ASP5
KeywordsTRANSPORT PROTEIN / helical protein / odorant molecules / antennae
Function / homology
Function and homology information


odorant binding / extracellular region
Similarity search - Function
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
N-BUTYL-BENZENESULFONAMIDE / Odorant binding protein ASP5
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsSpinelli, S. / Iovinella, I. / Lagarde, A. / Tegoni, M. / Pelosi, P. / Cambillau, C.
CitationJournal: To be Published
Title: Crystal structure of Apis mellifera odorant binding protein 5
Authors: Spinelli, S. / Iovinella, I. / Lagarde, A. / Tegoni, M. / Pelosi, P. / Cambillau, C.
History
DepositionMar 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Oct 16, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Odorant binding protein ASP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7643
Polymers14,3381
Non-polymers4272
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.695, 45.239, 70.882
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Odorant binding protein ASP5 / odorant binding protein 5


Mass: 14337.521 Da / Num. of mol.: 1 / Fragment: UNP residues 23-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apis mellifera (honey bee) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WRW2
#2: Chemical ChemComp-NBB / N-BUTYL-BENZENESULFONAMIDE


Mass: 213.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15NO2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20-25% PEG1500, MIB pH 3.7-4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.975
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 27, 2010
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.15→38.13 Å / Num. all: 42573 / Num. obs: 42573 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 17.5
Reflection shellResolution: 1.15→1.21 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.4 / Num. unique all: 6095 / % possible all: 97.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→38.13 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.036 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.038 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17253 2188 5 %RANDOM
Rwork0.15181 ---
obs0.15289 41327 99.3 %-
all-41327 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.071 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0 Å2
2---0.26 Å20 Å2
3---0.3 Å2
Refine analyzeLuzzati coordinate error free: 0.036 Å
Refinement stepCycle: LAST / Resolution: 1.15→38.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 28 254 1272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221096
X-RAY DIFFRACTIONr_bond_other_d0.0010.02762
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.9961486
X-RAY DIFFRACTIONr_angle_other_deg0.9131873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.475136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.63625.47253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62215208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.878155
X-RAY DIFFRACTIONr_chiral_restr0.0870.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021222
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02219
X-RAY DIFFRACTIONr_mcbond_it1.1211.5646
X-RAY DIFFRACTIONr_mcbond_other0.321.5255
X-RAY DIFFRACTIONr_mcangle_it1.95521060
X-RAY DIFFRACTIONr_scbond_it2.8593450
X-RAY DIFFRACTIONr_scangle_it4.4884.5422
X-RAY DIFFRACTIONr_rigid_bond_restr1.08231858
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 141 -
Rwork0.282 2886 -
obs--94.92 %

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