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- PDB-1kx9: ANTENNAL CHEMOSENSORY PROTEIN A6 FROM THE MOTH MAMESTRA BRASSICAE -

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Basic information

Entry
Database: PDB / ID: 1kx9
TitleANTENNAL CHEMOSENSORY PROTEIN A6 FROM THE MOTH MAMESTRA BRASSICAE
ComponentsCHEMOSENSORY PROTEIN A6
KeywordsLIPID TRANSPORT / ALL HELIX
Function / homologyAntennal chemosensory protein a6 / Insect odorant-binding protein A10/Ejaculatory bulb-specific protein 3 / Insect odorant-binding protein A10/Ejaculatory bulb-specific protein 3 / Insect odorant-binding protein A10/Ejaculatory bulb-specific protein 3 superfamily / Insect pheromone-binding family, A10/OS-D / Orthogonal Bundle / Mainly Alpha / ACETATE ION / Chemosensory protein
Function and homology information
Biological speciesMamestra brassicae (cabbage moth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsLartigue, A. / Campanacci, V. / Roussel, A. / Larsson, A.M. / Jones, T.A. / Tegoni, M. / Cambillau, C.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: X-ray structure and ligand binding study of a moth chemosensory protein
Authors: Lartigue, A. / Campanacci, V. / Roussel, A. / Larsson, A.M. / Jones, T.A. / Tegoni, M. / Cambillau, C.
#1: Journal: Eur.J.Biochem. / Year: 2001
Title: Chemosensory Protein from the Moth Mamestra brassicae. Expression and Secondary Structure from 1H and 15N NMR
Authors: Campanacci, V. / Mosbah, A. / Bornet, O. / Wechselberger, R. / Jacquin-Joly, E. / Cambillau, C. / Darbon, H. / Tegoni, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Recombinant Chemosensory Protein (CSP2) from the moth Mamestra brassicae: Crystallization and Preliminary Crystallographic Study
Authors: Campanacci, V. / Spinelli, S. / Lartigue, A. / Lewandowski, C. / Brown, K. / Tegoni, M. / Cambillau, C.
History
DepositionJan 31, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHEMOSENSORY PROTEIN A6
B: CHEMOSENSORY PROTEIN A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3084
Polymers26,1902
Non-polymers1182
Water4,972276
1
A: CHEMOSENSORY PROTEIN A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1542
Polymers13,0951
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHEMOSENSORY PROTEIN A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1542
Polymers13,0951
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.600, 49.700, 50.300
Angle α, β, γ (deg.)90.00, 110.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CHEMOSENSORY PROTEIN A6


Mass: 13094.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mamestra brassicae (cabbage moth) / Plasmid: pET22b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9NG96
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG5000MME 36%, Na Acetate, 0.2M, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8
Details: Campanacci, V., (2001) Acta Crystallogr., Sect.D, 57, 137.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
146 mg/mlprotein1drop
250 mMTris1droppH8.0
336 %PEG5000 MME1reservoir
40.2 Msodium acetate1reservoirpH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 6, 2001 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. all: 25956 / Num. obs: 25956 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 11.8
Reflection shellResolution: 1.65→1.75 Å / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 7.2 / Num. unique all: 4096 / % possible all: 97.6
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 25 Å / % possible obs: 93.3 %
Reflection shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.69 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
MLPHAREphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.65→14.93 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1011472.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1258 4.8 %RANDOM
Rwork0.204 ---
all-25956 --
obs-25956 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.0333 Å2 / ksol: 0.343558 e/Å3
Displacement parametersBiso mean: 19 Å2
Baniso -1Baniso -2Baniso -3
1-4.4 Å20 Å20.88 Å2
2---2.59 Å20 Å2
3----1.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→14.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1696 0 8 276 1980
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_mcbond_it0.711.5
X-RAY DIFFRACTIONc_mcangle_it1.112
X-RAY DIFFRACTIONc_scbond_it1.412
X-RAY DIFFRACTIONc_scangle_it2.232.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.271 212 4.9 %
Rwork0.234 4096 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4LIGAND_PAR.PAR
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor Rfree: 0.204 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05

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