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- PDB-3s0d: Apis mellifera OBP 14 in complex with the citrus odorant citralva... -

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Basic information

Entry
Database: PDB / ID: 3s0d
TitleApis mellifera OBP 14 in complex with the citrus odorant citralva (3,7-dimethylocta-2,6-dienenitrile)
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
(2Z)-3,7-dimethylocta-2,6-dienenitrile / OBP14
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 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 20, 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)13,7032
Polymers13,5541
Non-polymers1491
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.400, 37.860, 86.150
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-CTV / (2Z)-3,7-dimethylocta-2,6-dienenitrile / citralva


Mass: 149.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 1.95 Å3/Da / Density % sol: 36.9 %
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: 1.24→45.1 Å / Num. all: 30933 / Num. obs: 30933 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 12.7
Reflection shellResolution: 1.24→1.27 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2517 / % possible all: 99.6

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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: 1.24→43.08 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.354 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18346 922 3 %RANDOM
Rwork0.15869 ---
all0.15942 29803 --
obs0.15942 29803 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.281 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å20 Å2
2---0.26 Å2-0 Å2
3---0.19 Å2
Refine analyzeLuzzati coordinate error free: 0.046 Å
Refinement stepCycle: LAST / Resolution: 1.24→43.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 11 171 1125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221043
X-RAY DIFFRACTIONr_bond_other_d0.0010.02700
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9961422
X-RAY DIFFRACTIONr_angle_other_deg0.89131773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2195142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.36627.95544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.1815227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.358151
X-RAY DIFFRACTIONr_chiral_restr0.0840.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021128
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02161
X-RAY DIFFRACTIONr_mcbond_it1.0111.5639
X-RAY DIFFRACTIONr_mcbond_other0.3191.5253
X-RAY DIFFRACTIONr_mcangle_it1.6821063
X-RAY DIFFRACTIONr_scbond_it2.7143404
X-RAY DIFFRACTIONr_scangle_it4.2214.5346
X-RAY DIFFRACTIONr_rigid_bond_restr0.99531743
LS refinement shellResolution: 1.24→1.272 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.472 67 -
Rwork0.354 2160 -
obs-2160 100 %
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)
1-0.36331.20750.80832.23291.62693.20130.08440.01040.07020.3112-0.0874-0.00290.2948-0.02450.0030.0721-0.00190.00760.01750.00250.01616.0533.492129.5034
20.1057-0.4511-0.12323.0743-0.93170.29060.00690.01140.04880.0007-0.0227-0.08240.03310.05240.01580.03120.00270.00250.03150.00430.031218.212516.462724.5735
30.47150.45070.03141.6243-0.34882.25210.0186-0.01180.01450.0565-0.0565-0.1274-0.05490.10740.03790.01360.00170.0010.0282-0.00360.033519.017424.988631.5804
40.70080.09890.81990.5306-0.92021.2756-0.0543-0.14120.15210.11870.01770.0035-0.0945-0.03860.03660.03950.0076-0.00540.03-0.01430.047311.53924.105635.9701
51.23310.05720.28290.39690.39010.485-0.04320.04590.0813-0.0220.04970.0308-0.01650.0145-0.00650.0298-0.002500.02590.00490.032510.638324.240826.0629
63.5481-0.35761.1218-0.2779-0.57491.31610.03090.0543-0.194-0.07670.01840.04760.1078-0.0228-0.04930.0327-0.0106-0.01270.015-0.00420.05894.465614.825421.2097
73.62531.71842.59181.8068-1.03513.53470.2743-0.32280.1245-0.09350.03560.23130.4498-0.4586-0.30990.0475-0.0455-0.01760.06290.01130.0089-1.182510.577527.1311
86.2441.1699-2.77250.61670.01581.8048-0.2305-0.0783-0.1366-0.08960.1674-0.10140.2184-0.06810.06310.0678-0.04670.01710.0924-0.01590.00893.70913.102837.2966
9-0.7562-0.19040.57755.1013-2.25563.1290.0347-0.06430.0883-0.1115-0.00820.16410.261-0.2342-0.02640.0149-0.01050.00290.04960.00980.0456-3.576210.974637.2227
101.85170.2519-0.75641.293-0.20071.45170.0543-0.00960.0479-0.1060.04640.1640.0088-0.0842-0.10060.01640.0043-0.00740.03410.01920.0552-1.125125.488928.834
11-0.7446-0.72450.06754.9742-0.97532.69630.024-0.00360.0020.1132-0.02810.24950.0251-0.03050.00410.0147-0.00230.00490.0351-0.00090.04384.420919.152636.6715
120.96860.12970.83180.0654-0.20510.66140.0504-0.0042-0.0432-0.0167-0.0131-0.00890.07880.0224-0.03730.05220.00350.00090.02670.00040.018714.35979.896538.878
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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