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- PDB-3ogn: Crystal Structure of an Odorant-binding Protein from the Southern... -

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Basic information

Entry
Database: PDB / ID: 3ogn
TitleCrystal Structure of an Odorant-binding Protein from the Southern House Mosquito Complexed with an Oviposition Pheromone
ComponentsOdorant-binding protein
KeywordsTRANSPORT PROTEIN / helix bundle / Odorant-binding Protein
Function / homology
Function and homology information


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
Chem-3OG / Odorant-binding protein
Similarity search - Component
Biological speciesCulex quinquefasciatus (southern house mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMao, Y. / Clardy, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Crystal and solution structures of an odorant-binding protein from the southern house mosquito complexed with an oviposition pheromone.
Authors: Mao, Y. / Xu, X. / Xu, W. / Ishida, Y. / Leal, W.S. / Ames, J.B. / Clardy, J.
History
DepositionAug 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Odorant-binding protein
B: Odorant-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5158
Polymers28,7932
Non-polymers7226
Water7,548419
1
A: Odorant-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7825
Polymers14,3971
Non-polymers3854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Odorant-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7333
Polymers14,3971
Non-polymers3372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.915, 107.310, 38.529
Angle α, β, γ (deg.)90.00, 100.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Odorant-binding protein / / mosquito odorant binding protein


Mass: 14396.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Culex quinquefasciatus (southern house mosquito)
Gene: CpipJ_CPIJ007604 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8T6I2
#2: Chemical ChemComp-3OG / (1S)-1-[(2R)-6-oxotetrahydro-2H-pyran-2-yl]undecyl acetate / (5R,6S)-6-acetoy-5-hexadecanolide


Mass: 312.444 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H32O4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 20% (wt/vol) PEG 4,000, 100 mM HEPES, 200 mM MgCl2, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 68116 / Num. obs: 68116 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)% possible all
1.3-1.3595.5
1.35-1.496.3
1.4-1.4696.6
1.46-1.5497
1.54-1.6497.4
1.64-1.7698
1.76-1.9498.4
1.94-2.2298.9
2.22-2.899.3
2.8-5091.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→26.83 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.16 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17374 3426 5 %RANDOM
Rwork0.13201 ---
all0.13415 64639 --
obs0.13415 64639 96.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.795 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.16 Å2
2--0 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.3→26.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 48 419 2481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0222224
X-RAY DIFFRACTIONr_angle_refined_deg2.3661.9943018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2725276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34325.192104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20315422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.03156
X-RAY DIFFRACTIONr_chiral_restr0.1410.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211674
X-RAY DIFFRACTIONr_mcbond_it2.4611.51294
X-RAY DIFFRACTIONr_mcangle_it3.59322108
X-RAY DIFFRACTIONr_scbond_it5.3083930
X-RAY DIFFRACTIONr_scangle_it7.4654.5894
X-RAY DIFFRACTIONr_rigid_bond_restr2.87232224
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 235 -
Rwork0.159 4699 -
obs--94.78 %

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