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- PDB-3s0f: Apis mellifera OBP14 native apo, crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 3s0f
TitleApis mellifera OBP14 native apo, crystal form 2
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
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 27, 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
B: OBP14


Theoretical massNumber of molelcules
Total (without water)27,1072
Polymers27,1072
Non-polymers00
Water4,306239
1
A: OBP14


Theoretical massNumber of molelcules
Total (without water)13,5541
Polymers13,5541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OBP14


Theoretical massNumber of molelcules
Total (without water)13,5541
Polymers13,5541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.080, 75.380, 42.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-176-

HOH

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Components

#1: Protein OBP14 / odorant binding protein 14


Mass: 13553.611 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 1.88 Å3/Da / Density % sol: 34.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 30% PEG4000, 10 mM imidazole-malate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 11, 2011 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→45.2 Å / Num. all: 13308 / Num. obs: 13308 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 15.25 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 26.4
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 12 / Num. unique all: 732 / % possible all: 73.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
BUSTER2.9.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S0A

3s0a


Resolution: 2.03→37.69 Å / Cor.coef. Fo:Fc: 0.9304 / Cor.coef. Fo:Fc free: 0.9149 / Occupancy max: 1 / Occupancy min: 0.7 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 1014 7.62 %RANDOM
Rwork0.1937 ---
all0.1956 13305 --
obs0.1956 13305 --
Displacement parametersBiso max: 78.31 Å2 / Biso mean: 16.8 Å2 / Biso min: 3.09 Å2
Baniso -1Baniso -2Baniso -3
1--3.4805 Å20 Å20 Å2
2--0.7482 Å20 Å2
3---2.7323 Å2
Refine analyzeLuzzati coordinate error obs: 0.246 Å
Refinement stepCycle: LAST / Resolution: 2.03→37.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 0 239 2121
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d723SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes252HARMONIC5
X-RAY DIFFRACTIONt_it1902HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion264SEMIHARMONIC5
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_contact2626SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1902HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2559HARMONIC21.24
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion18.95
LS refinement shellResolution: 2.03→2.19 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2353 208 8.3 %
Rwork0.1989 2299 -
all0.2018 2507 -
obs-2299 -
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)
10-0.01750.02280.01940.00470.06830.0007-0.0009-0.00040.00010.00090.0001-0.0020.0011-0.00160.00270.00020.00040.0034-0.0038-0.008115.139725.944315.0521
20.05140.10540.02160.0651-0.072300.00040.0012-0.0041-0.0014-0.00040.00050.0035-0.00110-0.00250.002-0.004-0.00120.00310.000217.095611.357921.3563
30.02070.238-0.138300.066800.00070.00240.0024-0.0027-0.00170.00070.00160.00290.001-0.0059-0.00750.0090.0020.01010.001529.098824.392517.288
40.04870.0682-0.010400.079800.00050.0011-0.00080.0006-0.0002-0.0009-0.00070.0036-0.0003-0.0078-0.0057-0.0003-0.00040.00470.005534.141720.10125.6386
50.0082-0.02410.018500.02200.00030.0003-0.0006-0.0007-0.0002-0.0010.00120.0005-0.0001-0.00450.0011-0.00670.0040.0015-0.000727.66113.198122.4649
60.02410.0024-0.02230-0.00660.00440.00030.00080.00020.001-0.00080.0002-0.0014-0.00160.0004-0.00430.001-0.00220.0035-0.0017-0.000418.363326.067827.2791
70-0.0397-0.04050.0266-0.01450.05590.0002-0.0017-0.001500.0005-0.0004-0.00180-0.00070.00210.00080.0031-0.00180.0023-0.003240.109548.49836.157
80.00040.0213-0.02080.079-0.09350.01740.00010.0013-0.002-0.0015-0.00010.00030.0013-0.003100.00790.0050.0133-0.00750.001-0.003842.472433.65342.3428
900.0686-0.07370.0149-0.06560.0330.0009-0.00140.0028-0.0001-0.00180.0006-0.00040.00420.0009-0.00050.00380.0116-0.00110.0052-0.005454.161946.814538.3314
100.00480.0248-0.07750.0159-0.06450.0605-0.0005-0.0013-0.00050-0.0004-0.00130.00040.00210.00090.00090.00690.006-0.0007-0.0064-0.00259.159842.587446.5927
110-0.0430.04160.0124-0.04590.0217-0.00020.0015-0.00080.00020.0002-0.00120-0.000200.00520.003-0.00080.00020.0062-0.004452.777135.592943.5066
120-0.04020.035400.051800.00020.001-0.00040.00080.0005-0.00010.0007-0.0015-0.00070.00050.00490.0013-0.0017-0.0052-0.001843.383448.441948.326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - A|19}A1 - 19
2X-RAY DIFFRACTION2{A|20 - A|49}A20 - 49
3X-RAY DIFFRACTION3{A|50 - A|78}A50 - 78
4X-RAY DIFFRACTION4{A|79 - A|95}A79 - 95
5X-RAY DIFFRACTION5{A|96 - A|107}A96 - 107
6X-RAY DIFFRACTION6{A|108 - A|119}A108 - 119
7X-RAY DIFFRACTION7{B|1 - B|19}B1 - 19
8X-RAY DIFFRACTION8{B|20 - B|49}B20 - 49
9X-RAY DIFFRACTION9{B|50 - B|78}B50 - 78
10X-RAY DIFFRACTION10{B|79 - B|95}B79 - 95
11X-RAY DIFFRACTION11{B|96 - B|107}B96 - 107
12X-RAY DIFFRACTION12{B|108 - B|119}B108 - 119

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