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- PDB-3s0e: Apis mellifera OBP14 in complex with the odorant eugenol (2-metho... -

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Basic information

Entry
Database: PDB / ID: 3s0e
TitleApis mellifera OBP14 in complex with the odorant eugenol (2-methoxy-4(2-propenyl)-phenol)
ComponentsOBP14
KeywordsTRANSPORT PROTEIN / all helical protein / unknown odorant molecules / antennae
Function / homology
Function and homology information


odorant binding / extracellular region
Similarity search - Function
Pheromone/general odorant binding protein domain / Insect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-methoxy-4-(prop-2-en-1-yl)phenol / OBP14
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSpinelli, S. / Lagarde, A. / Iovinella, I. / Tegoni, M. / Pelosi, P. / Cambillau, C.
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2012
Title: Crystal structure of Apis mellifera OBP14, a C-minus odorant-binding protein, and its complexes with odorant molecules.
Authors: Spinelli, S. / Lagarde, A. / Iovinella, I. / Legrand, P. / Tegoni, M. / Pelosi, P. / Cambillau, C.
History
DepositionMay 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 1.3Nov 6, 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: OBP14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7182
Polymers13,5541
Non-polymers1641
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.610, 40.260, 91.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein OBP14 / odorant binding protein 14


Mass: 13553.611 Da / Num. of mol.: 1 / Fragment: UNP residues 18-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apis mellifera (honey bee) / Gene: NP_001035313 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q1W640
#2: Chemical ChemComp-EOL / 2-methoxy-4-(prop-2-en-1-yl)phenol / eugenol


Mass: 164.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.8
Details: 1.8-1.9 M tri-sodium citrate, 25 mM CHES, pH 9.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8265
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2011 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8265 Å / Relative weight: 1
ReflectionResolution: 1.6→45 Å / Num. all: 17204 / Num. obs: 17204 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 15
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1169 / % possible all: 92.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
BUSTER2.9.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S0A

3s0a


Resolution: 1.6→32.39 Å / Cor.coef. Fo:Fc: 0.9403 / Cor.coef. Fo:Fc free: 0.9413 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 890 5.18 %RANDOM
Rwork0.1899 ---
all0.1904 17183 --
obs0.1904 17183 --
Displacement parametersBiso max: 91.12 Å2 / Biso mean: 26.37 Å2 / Biso min: 10.76 Å2
Baniso -1Baniso -2Baniso -3
1-5.0029 Å20 Å20 Å2
2---6.1365 Å20 Å2
3---1.1335 Å2
Refine analyzeLuzzati coordinate error obs: 0.199 Å
Refinement stepCycle: LAST / Resolution: 1.6→32.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 12 139 1094
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d368SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes129HARMONIC5
X-RAY DIFFRACTIONt_it963HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion133SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1293SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d975HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg1312HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion17.79
LS refinement shellResolution: 1.6→1.7 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.247 138 5.24 %
Rwork0.2074 2497 -
all0.2093 2635 -
obs-2635 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10-0.0850.02930.0438-0.0460.04150.0003-0.00050.003-0.0012-0.00120.0016-0.00160.00120.00090.01580.0175-0.0062-0.013-0.0094-0.0034-2.5236-1.2336-12.3114
20.0172-0.09420.11060.0851-0.09540.06470.0008-0.00050.0007-0.0010.00060.0032-0.0025-0.0018-0.00140.00380.0089-0.0292-0.00850.0058-0.0036-6.795-13.1349-19.7384
30.03840.04820.0330.03680.03600-0.00150-0.0014-0.00180.00630.003-0.00110.0019-0.001-0.0027-0.0047-0.0024-0.01370.002-8.7118-21.2512-13.0302
40-0.0950.22620.0030.05920.04050.0001-0.0095-0.0046-0.0009-0.0010.00060.0041-0.00350.00090.00480.0178-0.0165-0.0042-0.0153-0.0056-0.8091-22.7215-9.2514
50.09780.03210.03980.04780.08050.05330.00060.00730.00030.00120.00120.0030.00170.0027-0.00180.01480.0262-0.0206-0.0144-0.03930.0073-0.3215-21.0566-18.3989
60.0330.00430.05110.0346-0.03260.0046-0.00060.00310.0018-0.00190.00030.00010.00070.00220.00030.004-0.0028-0.01160.00120.0222-0.00317.3821-12.4562-21.7971
70.0278-0.00380.01650.0025-0.00220.00150.00060.0015-0.00020.00120.0004-0.0006-0.0030.0021-0.0011-0.0046-0.0034-0.00140.00190.0037-0.001512.5709-9.673-16.5647
80-0.01330.0430.06310.103300-0.00040.0014-0.0011-0.00030.0011-0.0040.00160.0003-0.0091-0.0078-0.0119-0.0064-0.02950.00819.7593-3.7074-5.4056
90.087-0.04140.01980.0050.07170.002500.00020.00070.0012-0.002-0.0002-0.00120.00090.002-0.0160.0009-0.00810.0203-0.02940.000715.8085-12.6113-7.5771
100.0743-0.01810.0080.00020.09220.0143-0.0006-0.00010.0005-0.00420.0006-0.0013-0.00140.0030-0.00790.0184-0.01680.0041-0.04020.000410.6463-24.4883-18.0195
110.0919-0.06010.1250.01420.04310.02890.0005-0.00750.00190-0.0003-0.00070.00250.0016-0.0003-0.01810.0035-0.02850.0113-0.0333-0.00187.3803-17.7479-8.0322
120.06120.05330.03120.00590.12810.037800.0041-0.00070.00260.0021-0.0008-0.00450.0004-0.0021-0.00870.00570.00250.0175-0.0576-0.0175-2.8395-8.1337-4.29
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - A|10}A1 - 10
2X-RAY DIFFRACTION2{A|11 - A|20}A11 - 20
3X-RAY DIFFRACTION3{A|21 - A|30}A21 - 30
4X-RAY DIFFRACTION4{A|31 - A|40}A31 - 40
5X-RAY DIFFRACTION5{A|41 - A|50}A41 - 50
6X-RAY DIFFRACTION6{A|51 - A|60}A51 - 60
7X-RAY DIFFRACTION7{A|61 - A|70}A61 - 70
8X-RAY DIFFRACTION8{A|71 - A|80}A71 - 80
9X-RAY DIFFRACTION9{A|81 - A|90}A81 - 90
10X-RAY DIFFRACTION10{A|91 - A|100}A91 - 100
11X-RAY DIFFRACTION11{A|101 - A|110}A101 - 110
12X-RAY DIFFRACTION12{A|111 - A|119}A111 - 119

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