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- PDB-3s0b: Apis mellifera OBP14 in complex with the fluorescent probe 1-N-ph... -

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Basic information

Entry
Database: PDB / ID: 3s0b
TitleApis mellifera OBP14 in complex with the fluorescent probe 1-N-phenylnaphthylamine (NPN)
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
N-phenylnaphthalen-1-amine / OBP14
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 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)13,7732
Polymers13,5541
Non-polymers2191
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.380, 37.110, 89.750
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-FNA / N-phenylnaphthalen-1-amine


Mass: 219.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 1.99 Å3/Da / Density % sol: 38.17 %
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 8, 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: 1.22→45 Å / Num. all: 32858 / Num. obs: 32858 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 18
Reflection shellResolution: 1.22→1.25 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2387 / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S0A

3s0a


Resolution: 1.22→44.88 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.392 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18347 1666 5.1 %RANDOM
Rwork0.16697 ---
all0.16783 31192 --
obs0.16783 31192 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.081 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.06 Å2
Refine analyzeLuzzati coordinate error free: 0.044 Å
Refinement stepCycle: LAST / Resolution: 1.22→44.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 17 172 1132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221015
X-RAY DIFFRACTIONr_bond_other_d0.0040.02686
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9991374
X-RAY DIFFRACTIONr_angle_other_deg1.00131718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3115130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.5927.90743
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64515212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.165151
X-RAY DIFFRACTIONr_chiral_restr0.1170.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021111
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02166
X-RAY DIFFRACTIONr_mcbond_it1.1971.5624
X-RAY DIFFRACTIONr_mcbond_other0.4791.5248
X-RAY DIFFRACTIONr_mcangle_it1.9921029
X-RAY DIFFRACTIONr_scbond_it2.9033391
X-RAY DIFFRACTIONr_scangle_it4.5614.5343
X-RAY DIFFRACTIONr_rigid_bond_restr1.30931701
LS refinement shellResolution: 1.22→1.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 121 -
Rwork0.264 2260 -
obs-2260 99 %
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)
10.365-0.55640.16750.89210.05883.12680.04830.0281-0.0301-0.0873-0.05510.03250.12480.02010.00680.0795-0.00280.01530.0228-0.00060.045-15.022-16.85113.635
20.3604-0.08530.2931.71150.38230.3589-0.00110.0009-0.0009-0.041-0.00530.0495-0.0080.00130.00640.0535-0.00420.01660.0222-0.00160.0582-18.452-4.50819.706
30.7046-0.06-0.28590.6302-0.21861.0324-0.00210.06090.01120.0136-0.01860.0657-0.0783-0.08760.02060.03620.0032-0.00350.03660.00130.0545-19.1634.63513.014
40.9870.52640.74191.09150.79231.85530.02650.14260.0072-0.04480.0131-0.0209-0.08190.0627-0.03970.0377-0.00490.00480.0386-0.00320.039-11.6084.1288.428
50.578-0.46810.13620.84810.02061.02240.0159-0.02050.01140.00620.01130.0055-0.0270.0177-0.02720.04-0.00310.00660.0291-0.01010.0513-10.8533.22918.43
61.30230.45660.03350.9207-0.54031.6195-0.021-0.07230.02280.1173-0.1643-0.05280.12820.14630.18540.0712-0.00290.00360.05060.01860.0511-3.843-6.21321.663
70.81181.0803-0.35734.14670.79291.19470.0967-0.0437-0.0389-0.1118-0.1859-0.31890.09970.03910.08910.1440.06190.08890.05980.0410.11171.139-9.98615.772
84.2298-1.1404-2.88760.88660.48743.0429-0.07450.0482-0.07440.03950.04230.07180.18270.00860.03220.0525-0.00830.01710.0516-0.01750.0183-3.451-16.0864.925
90.01090.04240.07539.02861.00080.5906-0.0060.00350.01110.07820.009-0.19910.15630.0483-0.00290.05020.00160.01340.0799-0.05460.09043.884-8.556.322
102.1956-0.4629-0.35390.22460.06820.05740.02810.07470.15450.0693-0.007-0.0663-0.0078-0.0135-0.02110.048-0.0109-0.0090.0778-0.02760.06550.8874.76916.239
110.62041.0686-0.7183.01880.64223.83830.0241-0.0476-0.0168-0.0265-0.0226-0.0361-0.08530.1712-0.00160.01610.0379-0.02170.13-0.06440.0349-4.331-0.0997.367
127.92240.15371.35570.99770.94731.087-0.040.128-0.0760.09980.03840.01210.10220.04810.00160.1282-0.028-0.00190.0484-0.02040.0125-14.061-9.5244.308
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 10
2X-RAY DIFFRACTION2A11 - 20
3X-RAY DIFFRACTION3A21 - 30
4X-RAY DIFFRACTION4A31 - 40
5X-RAY DIFFRACTION5A41 - 50
6X-RAY DIFFRACTION6A51 - 60
7X-RAY DIFFRACTION7A61 - 70
8X-RAY DIFFRACTION8A71 - 80
9X-RAY DIFFRACTION9A81 - 90
10X-RAY DIFFRACTION10A91 - 100
11X-RAY DIFFRACTION11A101 - 109
12X-RAY DIFFRACTION12A110 - 119

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