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- PDB-2hlv: Bovine Odorant Binding Protein deswapped triple mutant -

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Basic information

Entry
Database: PDB / ID: 2hlv
TitleBovine Odorant Binding Protein deswapped triple mutant
ComponentsOdorant-binding protein
KeywordsTRANSPORT PROTEIN / Odorant binding protein / domain swapping
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 family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
3,6-BIS(METHYLENE)DECANOIC ACID / Odorant-binding protein
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSpinelli, S. / Tegoni, M. / Cambillau, C.
CitationJournal: Biochim.Biophys.Acta / Year: 2008
Title: Deswapping bovine odorant binding protein.
Authors: Ramoni, R. / Spinelli, S. / Grolli, S. / Conti, V. / Merli, E. / Cambillau, C. / Tegoni, M.
History
DepositionJul 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Odorant-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7573
Polymers18,4681
Non-polymers2882
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.501, 83.501, 48.964
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1073-

HOH

21A-1099-

HOH

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Components

#1: Protein Odorant-binding protein / OBP / Olfactory mucosa pyrazine-binding protein


Mass: 18468.350 Da / Num. of mol.: 1 / Mutation: Gly121+, Trp64Cys, His155Cys
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P07435
#2: Chemical ChemComp-LIK / 3,6-BIS(METHYLENE)DECANOIC ACID


Mass: 196.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 26% (W/V) PEG 8000, 200 mM Ammonium Sulfate and 10 mM Na Acetate (pH 4.8), protein at 7.5 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 23, 2003
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.65→57 Å / Num. all: 21290 / Num. obs: 21290 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.089 / Net I/σ(I): 5.2
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 20 % / Mean I/σ(I) obs: 2 / Rsym value: 0.28 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G85

1g85


Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.495 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21224 1091 5.1 %RANDOM
Rwork0.18451 ---
all0.18589 21260 --
obs0.18589 20168 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.493 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20 Å2
2---0.89 Å20 Å2
3---1.78 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1205 0 20 131 1356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221240
X-RAY DIFFRACTIONr_bond_other_d0.0030.021082
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.9461671
X-RAY DIFFRACTIONr_angle_other_deg0.78532531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8715148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41125.07963
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95415213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.919155
X-RAY DIFFRACTIONr_chiral_restr0.10.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021378
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02253
X-RAY DIFFRACTIONr_nbd_refined0.2030.2190
X-RAY DIFFRACTIONr_nbd_other0.210.2984
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2572
X-RAY DIFFRACTIONr_nbtor_other0.0820.2661
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.278
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3190.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2180.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.216
X-RAY DIFFRACTIONr_mcbond_it1.571.5970
X-RAY DIFFRACTIONr_mcbond_other0.2151.5308
X-RAY DIFFRACTIONr_mcangle_it1.66221191
X-RAY DIFFRACTIONr_scbond_it2.8753639
X-RAY DIFFRACTIONr_scangle_it3.5964.5480
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 75 -
Rwork0.186 1370 -
obs--99.93 %

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