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- PDB-1e02: Porcine Odorant Binding Protein Complexed with undecanal -

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Basic information

Entry
Database: PDB / ID: 100
TitlePorcine Odorant Binding Protein Complexed with undecanal
ComponentsODORANT-BINDING PROTEIN
KeywordsODORANT BINDING PROTEIN / LIPOCALINS
Function / homology
Function and homology information


odorant binding / small molecule binding / sensory perception of smell / extracellular space
Similarity search - Function
Lipocalin, OBP-like / Lipocalin / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
UNDECANAL / Odorant-binding protein
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.15 Å
AuthorsVincent, F. / Spinelli, S. / Cambillau, C. / Tegoni, M.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Complexes of Porcine Odorant Binding Protein with Odorant Molecules Belonging to Different Chemical Classes
Authors: Vincent, F. / Spinelli, S. / Ramoni, R. / Grolli, S. / Pelosi, P. / Cambillau, C. / Tegoni, M.
History
DepositionMar 9, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7834
Polymers35,4432
Non-polymers3412
Water3,639202
1
A: ODORANT-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8922
Polymers17,7211
Non-polymers1701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ODORANT-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8922
Polymers17,7211
Non-polymers1701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.779, 87.914, 92.507
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.16058, -0.18129, 0.97023), (-0.1754, 0.9621, 0.2088), (-0.97131, -0.20371, 0.1227)
Vector: -23.94837, 18.5359, 22.07671)

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Components

#1: Protein ODORANT-BINDING PROTEIN / PIG OBP


Mass: 17721.414 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: NOSE / Tissue: OLFACTORY EPITHELIUM / References: UniProt: P81245
#2: Chemical ChemComp-UNA / UNDECANAL


Mass: 170.292 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H22O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.8 / Details: 2M AMMONIUM SULFATE, AND 5% ISOPROPANOL, pH 7.80
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19 mg/mlprotein1drop
22 Mammonium sulfate1reservoir
35 %(v/v)iso-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.83→15 Å / Num. obs: 30761 / % possible obs: 97.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 13.5 Å2 / Rsym value: 0.047 / Net I/σ(I): 16
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.17 / % possible all: 96.9
Reflection
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 18 Å / % possible obs: 90.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.079
Reflection shell
*PLUS

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Processing

Software
NameVersionClassification
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: OTHER / Resolution: 2.15→18 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 100 / Cross valid method: THROUGHOUT / σ(F): 0
Details: N-TERMINUS FROM RESIDUE 1 TO 8, IN SUBUNIT A AND 1 - 10 IN SUBUNIT B, ARE NOT VISIBLE IN THE ELECTRON DENSITY, DUE TO FLEXIBILITY. ALTERNATE POSITIONS ARE PRESENT FOR SIDE CHAIN OF RESIDUES ...Details: N-TERMINUS FROM RESIDUE 1 TO 8, IN SUBUNIT A AND 1 - 10 IN SUBUNIT B, ARE NOT VISIBLE IN THE ELECTRON DENSITY, DUE TO FLEXIBILITY. ALTERNATE POSITIONS ARE PRESENT FOR SIDE CHAIN OF RESIDUES 19A, 39A, 114A. THE ATOMS CONCERNED HAVE OCCUPANCY BETWEEN 0.0 AND 1.0 AND A SEGID AC1 AND AC2 OFTEN, OCCUPANCY VALUES LOWER THAN 1.0 APPEARED TO JUSTIFY BETTER THE ELECTRON DENSITY. FOR THIS REASON WE HAVE KEPT THIS LOW OCCUPANCY FOR SEVERAL SIDE CHAIN ATOMS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 870 5 %RANDOM
Rwork0.192 ---
obs0.192 17404 90.7 %-
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1--6.11 Å20 Å20 Å2
2--3.2 Å20 Å2
3---2.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.15→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 24 202 2566
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.63
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.85
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.921.5
X-RAY DIFFRACTIONx_mcangle_it4.582
X-RAY DIFFRACTIONx_scbond_it3.382
X-RAY DIFFRACTIONx_scangle_it4.652.5
LS refinement shellResolution: 2.15→2.2 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.205 --
Rwork0.188 3048 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROPAR_SE.ODOR
X-RAY DIFFRACTION2XDICT_UND.PARXDICT_UND.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.85

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