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- PDB-1n8u: Chemosensory Protein in Complex with bromo-dodecanol -

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Basic information

Entry
Database: PDB / ID: 1n8u
TitleChemosensory Protein in Complex with bromo-dodecanol
Componentschemosensory protein
KeywordsLIPID BINDING PROTEIN
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 / BROMO-DODECANOL / Chemosensory protein
Function and homology information
Biological speciesMamestra brassicae (cabbage moth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCampanacci, V. / Lartigue, A. / Hallberg, B.M. / Jones, T.A. / Giudici-Orticoni, M.T. / Tegoni, M. / Cambillau, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Moth chemosensory protein exhibits drastic conformational changes and cooperativity on ligand binding.
Authors: Campanacci, V. / Lartigue, A. / Hallberg, B.M. / Jones, T.A. / Giudici-Orticoni, M.T. / Tegoni, M. / Cambillau, C.
History
DepositionNov 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: chemosensory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8914
Polymers13,0951
Non-polymers7963
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.529, 54.579, 33.226
Angle α, β, γ (deg.)90.00, 116.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein chemosensory protein /


Mass: 13094.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mamestra brassicae (cabbage moth) / Plasmid: PET-22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9NG96
#2: Chemical ChemComp-BDD / BROMO-DODECANOL


Mass: 265.230 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H25BrO
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 1.83 Å3/Da / Density % sol: 32.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 34% PEG 2000, 0.1M Na-cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
134 %mPEG200011
20.1 Msodium cacodylate11pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 9, 2000
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 7693 / Num. obs: 7693 / % possible obs: 81.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.6 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 11.8
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.087 / Mean I/σ(I) obs: 6.9 / % possible all: 71
Reflection
*PLUS
Lowest resolution: 28 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CSP complexed with bromo-dodecanol, form P 2<1>

Resolution: 1.8→38.63 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.883 / SU B: 4.873 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.215 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24571 683 9.2 %RANDOM
Rwork0.18379 ---
all0.19033 7693 --
obs0.19033 6730 80.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.038 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å2-1.21 Å2
2--0.9 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms820 0 42 110 972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021875
X-RAY DIFFRACTIONr_bond_other_d0.0010.02812
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9931160
X-RAY DIFFRACTIONr_angle_other_deg0.79431917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.962399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88415168
X-RAY DIFFRACTIONr_chiral_restr0.0860.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02921
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02159
X-RAY DIFFRACTIONr_nbd_refined0.2390.3226
X-RAY DIFFRACTIONr_nbd_other0.2070.3757
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2660.571
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1380.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2640.326
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.7410.517
X-RAY DIFFRACTIONr_mcbond_it0.7451.5497
X-RAY DIFFRACTIONr_mcangle_it1.4292796
X-RAY DIFFRACTIONr_scbond_it2.9533378
X-RAY DIFFRACTIONr_scangle_it4.5044.5364
LS refinement shellResolution: 1.801→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.178 552
Refinement TLS params.Method: refined / Origin x: 14.077 Å / Origin y: 0.058 Å / Origin z: 3.644 Å
111213212223313233
T0.0118 Å20.0051 Å20.0002 Å2-0.0024 Å20.0011 Å2--0.0052 Å2
L1.3981 °2-0.1289 °2-0.2328 °2-0.7931 °2-0.0837 °2--1.7231 °2
S0.0142 Å °-0.0344 Å °0.0006 Å °0.0133 Å °-0.0308 Å °-0.0504 Å °0.1025 Å °0.0854 Å °0.0166 Å °
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 28 Å / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.48
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å

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