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- PDB-1e06: Porcine Odorant Binding Protein Complexed with 5-methyl-2-(1-meth... -

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Basic information

Entry
Database: PDB / ID: 1000000
TitlePorcine Odorant Binding Protein Complexed with 5-methyl-2-(1-methylethyl)phenol
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 / 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
5-METHYL-2-(1-METHYLETHYL)PHENOL / Odorant-binding protein
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.12 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 10, 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 1.3Oct 9, 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)35,7434
Polymers35,4432
Non-polymers3002
Water2,810156
1
A: ODORANT-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8722
Polymers17,7211
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ODORANT-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8722
Polymers17,7211
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.076, 88.287, 93.588
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: (0.15613, -0.18642, 0.96998), (-0.18696, 0.9587, 0.21434), (-0.96988, -0.21482, 0.11483)
Vector: -23.97113, 18.52975, 22.7045)

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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-IPB / 5-METHYL-2-(1-METHYLETHYL)PHENOL


Mass: 150.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.12→24 Å / Num. obs: 23430 / % possible obs: 99 % / Redundancy: 3.2 % / Biso Wilson estimate: 17.6 Å2 / Rsym value: 0.029 / Net I/σ(I): 15
Reflection shellResolution: 2.12→2.15 Å / Redundancy: 3 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.068 / % possible all: 99.3
Reflection
*PLUS
Rmerge(I) obs: 0.029
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.168

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Processing

Software
NameVersionClassification
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: OTHER / Resolution: 2.12→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 100 / Cross valid method: THROUGHOUT / σ(F): 2
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. OFTEN, OCCUPANCY VALUES LOWER THAN 1.0 APPEARED TO JUSTIFY ...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. 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
Rfree0.255 1209 6.2 %RANDOM
Rwork0.213 ---
obs0.213 19603 98.2 %-
Displacement parametersBiso mean: 30.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 2.12→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 22 156 2518
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.55
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.29
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
LS refinement shellResolution: 2.12→2.17 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rwork0.225 3135 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROXDICT-THYM.TOP
X-RAY DIFFRACTION2XDICT_THYM.PAR
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 19759 / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.29

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