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- PDB-1gt5: Complexe of Bovine Odorant Binding Protein with benzophenone -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1gt5
TitleComplexe of Bovine Odorant Binding Protein with benzophenone
ComponentsODORANT-BINDING PROTEIN
KeywordsLIPOCALIN / BOVINE ODORANT BINDING PROTEIN
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
DIPHENYLMETHANONE / Odorant-binding protein
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsVincent, F. / Ramoni, R. / Spinelli, S. / Grolli, S. / Conti, V. / Cambillau, C. / Tegoni, M.
CitationJournal: Eur.J.Biochem. / Year: 2004
Title: Crystal Structures of Bovine Odorant-Binding Protein in Complex with Odorant Molecules.
Authors: Vincent, F. / Ramoni, R. / Spinelli, S. / Grolli, S. / Tegoni, M. / Cambillau, C.
History
DepositionJan 10, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)37,4214
Polymers37,0572
Non-polymers3642
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.589, 65.206, 42.153
Angle α, β, γ (deg.)90.00, 98.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ODORANT-BINDING PROTEIN / OBP / OLFACTORY MUCOSA PYRAZINE-BINDING PROTEIN


Mass: 18528.381 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: BENZOPHENONE AS LIGAND / Source: (natural) BOS TAURUS (domestic cattle) / Organ: NOSE / Tissue: RESPIRATORY EPITHELIUM / References: UniProt: P07435
#2: Chemical ChemComp-BZQ / DIPHENYLMETHANONE / BENZENE, BENZOYL- / BENZOPHENONE (8CI) / BENZOYLBENZENE / DIPHENYL KETONE / KETONE, DIPHENYL / METHANONE, DIPHENYL- (9CI) / PHENYL KETONE / WLN: RVR


Mass: 182.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H10O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 1.97 Å3/Da / Density % sol: 37 %
Crystal growpH: 4.2 / Details: pH 4.20
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
228-32 %(v/v)ethanol1reservoir
350 mMcitrate1reservoirpH5.4

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 2000 / Details: MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.08→19 Å / Num. obs: 17304 / % possible obs: 86.5 % / Redundancy: 2 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.0541 / Net I/σ(I): 10.6
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 3.4 / % possible all: 86.5
Reflection
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 20 Å / % possible obs: 86.4 % / Redundancy: 2 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Rmerge(I) obs: 0.242

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OBP

1obp


Resolution: 2.08→17.9 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1408 9.1 %RANDOM
Rwork0.188 ---
obs0.188 15515 86.6 %-
Displacement parametersBiso mean: 35 Å2
Refinement stepCycle: LAST / Resolution: 2.08→17.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2582 0 28 96 2706
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.08→2.21 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.272 215 9.4 %
Rwork0.241 2083 -
obs--77.4 %
Refinement
*PLUS
Lowest resolution: 18 Å / Num. reflection obs: 15517
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68

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