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- PDB-3rzs: Apis mellifera OBP14 in complex with Ta6Br14 -

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Basic information

Entry
Database: PDB / ID: 3rzs
TitleApis mellifera OBP14 in complex with Ta6Br14
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
HEXATANTALUM DODECABROMIDE / OBP14
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 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 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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)15,5982
Polymers13,5541
Non-polymers2,0451
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.260, 38.030, 86.810
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-TBR / HEXATANTALUM DODECABROMIDE / DODECABROMOHEXATANTALUM


Mass: 2044.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br12Ta6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.03 Å3/Da / Density % sol: 39.27 %
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: 1.2545
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2010
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2545 Å / Relative weight: 1
ReflectionResolution: 1.88→33.3 Å / Num. all: 9512 / Num. obs: 9512 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 22.76 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 20.2
Reflection shellResolution: 1.88→1.98 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5.7 / Num. unique all: 1340 / % possible all: 98.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
BUSTER2.9.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.88→31.06 Å / Cor.coef. Fo:Fc: 0.8972 / Cor.coef. Fo:Fc free: 0.8912 / Occupancy max: 1 / Occupancy min: 0.6 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 471 5 %RANDOM
Rwork0.2062 ---
all0.207 9416 --
obs0.207 9416 --
Displacement parametersBiso max: 89.62 Å2 / Biso mean: 31.78 Å2 / Biso min: 14.28 Å2
Baniso -1Baniso -2Baniso -3
1--17.4047 Å20 Å20 Å2
2--7.4498 Å20 Å2
3---9.9549 Å2
Refine analyzeLuzzati coordinate error obs: 0.239 Å
Refinement stepCycle: LAST / Resolution: 1.88→31.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 18 61 1022
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d363SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes35HARMONIC2
X-RAY DIFFRACTIONt_gen_planes126HARMONIC5
X-RAY DIFFRACTIONt_it989HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion138SEMIHARMONIC5
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_contact1218SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d989HARMONIC20.011
X-RAY DIFFRACTIONt_angle_deg1462HARMONIC21.44
X-RAY DIFFRACTIONt_omega_torsion3.81
X-RAY DIFFRACTIONt_other_torsion19.08
LS refinement shellResolution: 1.88→2.1 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2484 131 4.98 %
Rwork0.2203 2502 -
all0.2217 2633 -
obs-9416 -
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)
10-0.0627-0.04060.03090.03120.04910.0004-0.0004-0.0035-0.0007-0.00090.0012-0.0002-0.00310.00050.01050.01650.0043-0.0006-0.0068-0.002116.08523.071829.8309
20.0034-0.0235-0.00020.03490.04180.031700.0014-0.0005-0.00070.0002-0.00040.00160.0018-0.00030.0042-0.0001-0.0007-0.0029-0.00380.001718.454315.953924.1874
300.0368-0.00270-0.00640-0.00050.0011-0.0002-0.00050.0004-0.0017-0.00080.00160-0.0001-0.0039-0.0076-0.0042-0.00680.002619.522723.989831.4135
400.0450.07360.02330.0590.00560.0001-0.00280.00110.0007-0.0010.0008-0.00180.00060.00090.00580.0016-0.0156-0.01470.00120.005812.050123.693835.9125
50.0037-0.00970.11420.0191-0.00160.00680.00060.00070.0008-0.00040.0012-0.00030.00160.0004-0.00180.00450.0031-0.0092-0.00790.01250.001311.153523.233926.4641
60.01680.03750.02590.0265-0.00820-0.00020.001-0.0005-0.0005-0.00020.00060-0.00110.0004-0.003-0.0016-0.0082-0.00660.00490.00624.661314.256421.9528
70.00210.01760.038200.002300.00020.00080.00050.0005-0.00030.00050.0007-0.00180.00020.0002-0.0039-0.0043-0.00190.00290-0.451210.678126.7995
80.0064-0.0015-0.015600.009300.0001-0.00080.0004-0.0015-0.0002-0.00130.0019-0.0010.00010-0.00540.002-0.00360.00230.00143.65533.157837.5638
90.019-0.0157-0.00610.0132-0.00790.008500.00030.0023-0.00050.0003-0.0001-0.00070.0001-0.0003-0.002-0.00430.00450.00010.00450.0071-3.449211.412536.6884
100.0104-0.02570.02220.003-0.00700.00020.00010.0003-0.001300.0007-0.0012-0.0004-0.0002-0.00540.0028-0.0062-0.00270.00260.0042-0.499425.025728.7985
1100.02960.00910.0120.0170.01930-0.00120.0010.00110.00020.00040.0005-0.0013-0.0002-0.003-0.00350.0048-0.00470.0010.00054.54317.530336.7108
120.0149-0.0127-0.01740.00320.02290.00220.00030.00060.00020.00040.000300.00120.0004-0.00060.00090.0015-0.0022-0.00090.00430.000916.01399.155338.7057
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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