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- PDB-1dzm: Porcine Odorant Binding Protein Complexed with benzoic acid pheny... -

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Basic information

Entry
Database: PDB / ID: 1dzm
TitlePorcine Odorant Binding Protein Complexed with benzoic acid phenylmethylester
ComponentsODORANT-BINDING PROTEIN
KeywordsODORANT BINDING PROTEIN / LIPOCALINS
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
BENZOIC ACID PHENYLMETHYLESTER / Odorant-binding protein
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.93 Å
AuthorsVincent, F. / Spinelli, S. / Ramoni, R. / Grolli, S. / Pelosi, P. / 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 3, 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 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval

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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)35,8674
Polymers35,4432
Non-polymers4242
Water4,594255
1
A: ODORANT-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9342
Polymers17,7211
Non-polymers2121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ODORANT-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9342
Polymers17,7211
Non-polymers2121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.009, 88.679, 93.163
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: (0.14459, 0.0159, -0.98936), (-0.19005, 0.9817, -0.012), (0.97107, 0.18976, 0.14496)
Vector: 24.06054, -20.85672, 16.88272)

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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-BZM / BENZOIC ACID PHENYLMETHYLESTER / Benzyl benzoate


Mass: 212.244 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12O2 / Comment: medication*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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 growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PROTEIN (0.47MM) IS INCUBATED WITH 10MM OF PYRAZINE, THE COMPLEX WAS CRYSTALLISED FROM 2M AMMONIUM SULFATE, AND 5% ISOPROPANOL IN HANGING DROPS, AT 20 DEGREES, 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: Sep 24, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.93→15 Å / Num. obs: 26679 / % possible obs: 99.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 30.5 Å2 / Rsym value: 0.067 / Net I/σ(I): 13.7
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.27 / % possible all: 99.9
Reflection
*PLUS
Redundancy: 3.35 % / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.258

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.93→15 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1367052.68 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: N-TERMINUS FROM RESIDUE 1 TO 8, IN SUBUNIT A AND 1 TO 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 TO 10 IN SUBUNIT B, ARE NOT VISIBLE IN THE ELECTRON DENSITY, DUE TO FLEXIBILITY. ALTERNATE POSITIONS ARE PRESENT FOR SIDE CHAIN OF RESIDUES 19A, 79A, 81A, 123A, 76B 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
Rfree0.246 1337 5 %RANDOM
Rwork0.235 ---
obs0.235 26638 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.53 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 44.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å20 Å2
2--0.81 Å20 Å2
3---0.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.93→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 32 255 2627
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
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: 1.93→2.05 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 213 4.9 %
Rwork0.285 4171 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3XDICT_BZB.PARXDICT_BZB.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 25301 / Rfactor Rfree: 0.256 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.66
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91

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