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- PDB-2pql: Crystal Structure of Anopheles gambiae D7R4-tryptamine complex -

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Basic information

Entry
Database: PDB / ID: 2pql
TitleCrystal Structure of Anopheles gambiae D7R4-tryptamine complex
ComponentsD7r4 protein
KeywordsTRANSPORT PROTEIN / ALL-HELICAL / ODORANT-BINDING PROTEIN
Function / homology
Function and homology information


odorant binding / vasodilation / sensory perception of smell / 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
2-(1H-INDOL-3-YL)ETHANAMINE / Short form salivary protein D7R4
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsAndersen, J.F. / Mans, B.J. / Calvo, E. / Ribeiro, J.M.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The Crystal Structure of D7r4, a Salivary Biogenic Amine-binding Protein from the Malaria Mosquito Anopheles gambiae.
Authors: Mans, B.J. / Calvo, E. / Ribeiro, J.M. / Andersen, J.F.
History
DepositionMay 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D7r4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2602
Polymers17,1001
Non-polymers1601
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.101, 63.101, 42.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein D7r4 protein / D7-related 4 protein


Mass: 17099.857 Da / Num. of mol.: 1 / Fragment: unp residues 22-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Strain: G3 / Gene: D7r4 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9BIH3
#2: Chemical ChemComp-TSS / 2-(1H-INDOL-3-YL)ETHANAMINE / TRYPTAMINE


Mass: 160.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 298 K / pH: 8
Details: 20 % PEG 6000, 0.1 M Tris HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9790981
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2006 / Details: ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR
RadiationMonochromator: SI 111, SAGITALLY FOCUSED SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9790981 Å / Relative weight: 1
ReflectionResolution: 2.2→63.12 Å / Num. obs: 8615 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 24.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 8 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 16.83 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→31.55 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.905 / SU B: 10.065 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.263 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 407 4.7 %RANDOM
Rwork0.172 ---
obs0.176 8601 99.3 %-
all-8660 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.2→31.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1185 0 12 121 1318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221224
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.9871646
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg17.7855143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2132460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29515237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.001159
X-RAY DIFFRACTIONr_chiral_restr0.0880.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02912
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.2561
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.2845
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.298
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.219
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7611.5737
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.56921171
X-RAY DIFFRACTIONr_scbond_it4.5793532
X-RAY DIFFRACTIONr_scangle_it6.6564.5475
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 35 -
Rwork0.161 573 -
obs--92.82 %
Refinement TLS params.Method: refined / Origin x: 8.5132 Å / Origin y: -22.3834 Å / Origin z: 0.7297 Å
111213212223313233
T-0.0453 Å20.0009 Å2-0.0294 Å2--0.0841 Å2-0.0223 Å2---0.0609 Å2
L3.2493 °20.4749 °21.6081 °2-1.0201 °20.6602 °2--3.1253 °2
S-0.3014 Å °0.0181 Å °0.3971 Å °-0.1873 Å °0.06 Å °0.0344 Å °-0.3724 Å °-0.0958 Å °0.2415 Å °

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