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- PDB-2qeh: Crystal Structure of Anopheles gambiae D7r4-serotonin complex -

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Basic information

Entry
Database: PDB / ID: 2qeh
TitleCrystal Structure of Anopheles gambiae D7r4-serotonin complex
ComponentsD7R4 Protein
KeywordsLIGAND BINDING PROTEIN / All-helical / Odorant-binding protein
Function / homology
Function and homology information


odorant binding / vasodilation / sensory perception of smell / extracellular space
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
SEROTONIN / Short form salivary protein D7R4
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.102 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
DepositionJun 25, 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
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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)17,2762
Polymers17,1001
Non-polymers1761
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.358, 63.358, 42.617
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
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-SRO / SEROTONIN / 3-(2-AMINOETHYL)-1H-INDOL-5-OL


Mass: 176.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20 %PEG 6000, 0.1 M Tris HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792601 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2006 / Details: mirrors
RadiationMonochromator: Si 111, Sagitally focused Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792601 Å / Relative weight: 1
ReflectionResolution: 2.102→63.37 Å / Num. all: 9976 / Num. obs: 9976 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rmerge(I) obs: 0.07 / Χ2: 1.197 / Net I/σ(I): 16.3
Reflection shellResolution: 2.102→2.18 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.409 / Num. unique all: 997 / Χ2: 1.865 / % possible all: 98.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
EPICS-baseddata aquisition systemdata collection
HKL-3000data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.102→63.37 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.792 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 478 4.8 %RANDOM
Rwork0.193 ---
obs0.196 9972 99.61 %-
all-9972 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.102→63.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1193 0 13 121 1327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221233
X-RAY DIFFRACTIONr_angle_refined_deg0.9651.9891658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3955144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2022460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57715240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.435159
X-RAY DIFFRACTIONr_chiral_restr0.0880.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02919
X-RAY DIFFRACTIONr_nbd_refined0.2450.3563
X-RAY DIFFRACTIONr_nbtor_refined0.3190.5854
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.5156
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.314
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3240.517
X-RAY DIFFRACTIONr_mcbond_it3.6251.5747
X-RAY DIFFRACTIONr_mcangle_it4.50621179
X-RAY DIFFRACTIONr_scbond_it6.33544
X-RAY DIFFRACTIONr_scangle_it8.6874.5479
LS refinement shellResolution: 2.102→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 34 -
Rwork0.207 697 -
obs-731 98.52 %
Refinement TLS params.Method: refined / Origin x: 26.5771 Å / Origin y: -9.7112 Å / Origin z: -3.2071 Å
111213212223313233
T-0.0589 Å2-0.0032 Å2-0.0272 Å2--0.0805 Å20.0146 Å2---0.0899 Å2
L0.6576 °2-0.0898 °20.1304 °2-1.563 °20.9743 °2--1.3926 °2
S0.025 Å °-0.0299 Å °-0.0513 Å °-0.0151 Å °-0.095 Å °0.0439 Å °-0.0997 Å °-0.0139 Å °0.0699 Å °

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