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- PDB-1hn2: CRYSTAL STRUCTURE OF BOVINE OBP COMPLEXED WITH AMINOANTHRACENE -

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Basic information

Entry
Database: PDB / ID: 1hn2
TitleCRYSTAL STRUCTURE OF BOVINE OBP COMPLEXED WITH AMINOANTHRACENE
ComponentsODORANT-BINDING PROTEIN
KeywordsPROTEIN BINDING / olfaction / odorant binding protein / aminoanthracene
Function / homology
Function and homology information


odorant binding / small molecule binding / sensory perception of smell / extracellular space
Similarity search - Function
Lipocalin, OBP-like / Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
(3R)-oct-1-en-3-ol / ANTHRACEN-1-YLAMINE / Odorant-binding protein
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 1.8 Å
AuthorsVincent, F. / Spinelli, S. / Tegoni, M. / Cambillau, C.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: The insect attractant 1-octen-3-ol is the natural ligand of bovine odorant-binding protein.
Authors: Ramoni, R. / Vincent, F. / Grolli, S. / Conti, V. / Malosse, C. / Boyer, F.D. / Nagnan-Le Meillour, P. / Spinelli, S. / Cambillau, C. / Tegoni, M.
History
DepositionDec 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 5, 2014Group: Non-polymer description
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Remark 600heterogen The Native Bovine OBP has a natural ligand Octene-3-ol (PDB ID 1G85). In this experiment, ...heterogen The Native Bovine OBP has a natural ligand Octene-3-ol (PDB ID 1G85). In this experiment, the native Bovine OBP was soaked with 2mM Aminoanthracene, which removed all of the natural ligand in cavity A (giving all Aminoantracene atoms occupancy 1.0) but left 40% of the natural ligand in cavity B. The occupancy of aminoanthracene atoms in cavity B was 0.60 because of the presence of octene-3-ol, with the R and S enantiomers each having occupancies of 0.20.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,5715
Polymers37,0572
Non-polymers5153
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-18 kcal/mol
Surface area16380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.589, 65.091, 42.249
Angle α, β, γ (deg.)90.00, 98.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ODORANT-BINDING PROTEIN / OBP


Mass: 18528.381 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P07435
#2: Chemical ChemComp-ANC / ANTHRACEN-1-YLAMINE / AMINOANTHRACENE


Mass: 193.244 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11N
#3: Chemical ChemComp-3OL / (3R)-oct-1-en-3-ol


Mass: 128.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growpH: 5.7
Details: dialysys against 38% ethanol in 25 mM sodium Citrate at 4 degrees, pH 5.7
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.4 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein11
228-32 %ethanol12
350 mMcitrate12pH5.4

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 28, 2000
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→17 Å / Num. obs: 26203 / % possible obs: 92 % / Redundancy: 2.8 % / Biso Wilson estimate: 21.4 Å2 / Rsym value: 5.2 / Net I/σ(I): 8.5
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.44 / % possible all: 85.4
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 18 Å / % possible obs: 92 % / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.84 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
CNSrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: molecular replacement
Starting model: 1OBP

1obp


Resolution: 1.8→9.95 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1113369.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1231 4.8 %RANDOM
Rwork0.202 ---
obs0.202 25449 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 73.09 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.52 Å20 Å2-1.19 Å2
2---5.32 Å20 Å2
3---7.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.8→9.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 39 120 2740
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 200 4.9 %
Rwork0.289 3866 -
obs--88.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAramPROTEIN.TOP
X-RAY DIFFRACTION2LIG.PARamWATER.TOP
X-RAY DIFFRACTION4WATER_REP.PARAM
X-RAY DIFFRACTION3LIG.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 15530 / % reflection Rfree: 4.8 % / Rfactor obs: 0.21 / Rfactor Rfree: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.48
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.325 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.289

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