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- PDB-1dzk: Porcine Odorant Binding Protein Complexed with pyrazine (2-isobut... -

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Basic information

Entry
Database: PDB / ID: 1dzk
TitlePorcine Odorant Binding Protein Complexed with pyrazine (2-isobutyl-3-metoxypyrazine)
ComponentsODORANT-BINDING PROTEIN
KeywordsTRANSPORT / LIPOCALIN / OLFACTION / SENSORY TRANSDUCTION
Function / homology
Function and homology information


odorant binding / response to stimulus / 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
2-ISOBUTYL-3-METHOXYPYRAZINE / Odorant-binding protein
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.48 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 1, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Version format compliance

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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)35,7754
Polymers35,4432
Non-polymers3322
Water5,044280
1
A: ODORANT-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8882
Polymers17,7211
Non-polymers1661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ODORANT-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8882
Polymers17,7211
Non-polymers1661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.169, 88.385, 93.760
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: (0.15526, 0.00223, -0.98787), (-0.16758, 0.98556, -0.02412), (0.97356, 0.16929, 0.15339)
Vector: 24.25345, -20.79514, 17.65045)

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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-PRZ / 2-ISOBUTYL-3-METHOXYPYRAZINE


Mass: 166.220 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.8
Details: PROTEIN (0.47MM) IS INCUBATED WITH 10MM OF PYRAZINE., 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: ESRF / Beamline: ID14-2 / Wavelength: 0.9465
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9465 Å / Relative weight: 1
ReflectionResolution: 1.48→25 Å / Num. obs: 56300 / % possible obs: 92.6 % / Redundancy: 2.72 % / Biso Wilson estimate: 20.9 Å2 / Rsym value: 0.056 / Net I/σ(I): 14
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.45 / % possible all: 92.3
Reflection
*PLUS
Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 92.3 % / Rmerge(I) obs: 0.093

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.48→12 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1300053.96 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: N-TERMINUS FROM RESIDUE 1 - 9, IN SUBUNIT A AND B, ARE NOT VISIBLE IN THE ELECTRON DENSITY, DUE TO FLEXIBILITY. ALTERNATE POSITIONS ARE PRESENT FOR SIDE CHAIN OF RESIDUES 19A, 39A, 57A, 79A, ...Details: N-TERMINUS FROM RESIDUE 1 - 9, IN SUBUNIT A AND B, ARE NOT VISIBLE IN THE ELECTRON DENSITY, DUE TO FLEXIBILITY. ALTERNATE POSITIONS ARE PRESENT FOR SIDE CHAIN OF RESIDUES 19A, 39A, 57A, 79A, 98A, 114A, 129A, 133A, 147A, 19B, 52B, 53B, 77B, 89B, 114B, 143B. 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
Rfree0.242 1684 3 %RANDOM
Rwork0.226 ---
obs0.226 50223 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 90.17 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso mean: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.4 Å20 Å20 Å2
2---0.52 Å20 Å2
3---3.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.48→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2344 0 24 280 2648
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.58
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: 1.48→1.56 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 280 3.2 %
Rwork0.311 8594 -
obs--89.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3XDICT_PYR.PARXDICT_PYR.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.58

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