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- PDB-1obp: ODORANT-BINDING PROTEIN FROM BOVINE NASAL MUCOSA -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1obp
TitleODORANT-BINDING PROTEIN FROM BOVINE NASAL MUCOSA
ComponentsODORANT-BINDING PROTEIN
KeywordsODORANT-BINDING PROTEIN / OLFACTION / NOSE / TRANSPORT / LIPOCALIN
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
Odorant-binding protein
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsTegoni, M. / Cambillau, C.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Domain swapping creates a third putative combining site in bovine odorant binding protein dimer
Authors: Tegoni, M. / Ramoni, R. / Bignetti, E. / Spinelli, S. / Cambillau, C.
#1: Journal: J.Biotechnol. / Year: 1993
Title: Preparation of an Affinity Resin for Odorants by Coupling Odorant Binding Protein from Bovine Nasal Mucosa to Sepharose 4B
Authors: Bignetti, E. / Bussolati, L. / Ramoni, R. / Grolli, S. / Donofrio, G.
#2: Journal: Eur.J.Biochem. / Year: 1985
Title: Purification and Characterisation of an Odorant-Binding Protein from Cow Nasal Tissue
Authors: Bignetti, E. / Cavaggioni, A. / Pelosi, P. / Persaud, K.C. / Sorbi, R.T. / Tirindelli, R.
#3: Journal: Biochem.J. / Year: 1982
Title: Identification of a Specific Olfactory Receptor for 2-Isobutyl-3-Methoxypyrazine
Authors: Pelosi, P. / Baldaccini, N.E. / Pisanelli, A.M.
History
DepositionJan 14, 1996Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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
B: ODORANT-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)36,91584
Polymers36,9152
Non-polymers082
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-38 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.900, 65.500, 42.700
Angle α, β, γ (deg.)90.00, 98.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.294, -0.342, -0.893), (-0.273, -0.865, 0.421), (-0.916, 0.368, 0.161)
Vector: 30.53137, 14.56698, 19.0032)

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Components

#1: Protein ODORANT-BINDING PROTEIN / OBP


Mass: 18457.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: NOSE / Tissue: RESPIRATORY EPITHELIUM / References: UniProt: P07435
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 82 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsRESIDUES NAMED UNX ARE PSEUDO CARBON ATOMS USED TO MODEL AN UNKNOWN LIGAND. TO ALLOW ATOM OVERLAP, ...RESIDUES NAMED UNX ARE PSEUDO CARBON ATOMS USED TO MODEL AN UNKNOWN LIGAND. TO ALLOW ATOM OVERLAP, SCATTERING FACTORS HAVE BEEN SET TO 20% OF THE NORMAL VALUE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 40 %
Crystal growpH: 5.7 / Details: pH 5.7
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Conc.: 35-45 % / Common name: ethanol

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: May 26, 1995
RadiationMonochromator: MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 20232 / % possible obs: 94.6 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.045

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 2→6 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.247 -5 %
Rwork0.164 --
obs0.164 18470 -
Displacement parametersBiso mean: 30.5 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3158 0 82 768 4008
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.53
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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