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- PDB-1hqp: CRYSTAL STRUCTURE OF A TRUNCATED FORM OF PORCINE ODORANT-BINDING ... -

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Basic information

Entry
Database: PDB / ID: 1hqp
TitleCRYSTAL STRUCTURE OF A TRUNCATED FORM OF PORCINE ODORANT-BINDING PROTEIN
ComponentsODORANT-BINDING PROTEIN
KeywordsSIGNALING PROTEIN / lipocalin / dimer / ligand-binding site / access to the binding site
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 / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
2-ISOBUTYL-3-METHOXYPYRAZINE / Odorant-binding protein
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPerduca, M. / Mancia, F. / Del Giorgio, R. / Monaco, H.L.
CitationJournal: Proteins / Year: 2001
Title: Crystal structure of a truncated form of porcine odorant-binding protein.
Authors: Perduca, M. / Mancia, F. / Del Giorgio, R. / Monaco, H.L.
History
DepositionDec 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
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_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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ODORANT-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8882
Polymers17,7211
Non-polymers1661
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.180, 44.140, 41.240
Angle α, β, γ (deg.)90.00, 107.03, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe asymmetric unit is a monomer. The dimer is generated by the crystallographic two-fold axis

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Components

#1: Protein ODORANT-BINDING PROTEIN


Mass: 17721.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: NASAL MUCOSA / References: UniProt: P81245
#2: Chemical ChemComp-PRZ / 2-ISOBUTYL-3-METHOXYPYRAZINE


Mass: 166.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O
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: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 293 K / Method: microdialysis / pH: 7.5
Details: Ammonium sulfate, Tris, ethylene glycol, pH 7.5, MICRODIALYSIS, temperature 293K
Crystal
*PLUS
Density % sol: 44 %
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein11
20.05 MTris12
33 %ethylene glycol12
42.9 Mammonium sulfate12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Feb 15, 1992 / Details: graphite monochromator
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. all: 14835 / Num. obs: 5662 / % possible obs: 80 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.16 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 31
Reflection shellResolution: 2.3→2.5 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 10.1 / Num. unique all: 1005 / % possible all: 64
Reflection
*PLUS
% possible obs: 80 % / Num. measured all: 14835 / Rmerge(I) obs: 0.0466
Reflection shell
*PLUS
% possible obs: 64 % / Num. unique obs: 1005 / Rmerge(I) obs: 0.1072

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Processing

Software
NameClassification
X-GENdata scaling
X-GENdata reduction
AMoREphasing
TNTrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A3Y

1a3y


Resolution: 2.3→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rwork0.204 ---
obs0.204 5620 80.4 %-
Rfree-0 -R-free was not calculated
all-6990 --
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 12 0 1191
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.27
X-RAY DIFFRACTIONt_bond_d0.004
X-RAY DIFFRACTIONt_dihedral_angle_d16.338
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.338

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