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- PDB-3dy9: Crystal structure of AeD7 potassium bromide soak -

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Basic information

Entry
Database: PDB / ID: 3dy9
TitleCrystal structure of AeD7 potassium bromide soak
ComponentsD7 protein
Keywordsodorant-binding protein / all-helical / secreted / Allergen
Function / homology
Function and homology information


odorant binding / regulation of defense response to virus / IgE binding / vasodilation / sensory perception of smell / toxin activity / 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
BROMIDE ION / Long form salivary protein D7L1
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsAndersen, J.F. / Calvo, E. / Mans, B.J. / Ribeiro, J.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Multifunctionality and mechanism of ligand binding in a mosquito antiinflammatory protein
Authors: Calvo, E. / Mans, B.J. / Ribeiro, J.M. / Andersen, J.F.
History
DepositionJul 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Mar 31, 2021Group: Derived calculations / Source and taxonomy / Category: entity_src_gen / struct_site
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D7 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,24814
Polymers35,1181
Non-polymers1,13013
Water8,557475
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.757, 66.062, 52.387
Angle α, β, γ (deg.)90.000, 113.270, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein D7 protein / Allergen Aed a 2


Mass: 35117.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Strain: Liverpool / Gene: D7 / Plasmid: VR2001 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P18153
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16-20% PEG-6000, 0.1 M Tris HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91959 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2006
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91959 Å / Relative weight: 1
ReflectionRedundancy: 7.7 % / Av σ(I) over netI: 8.9 / Number: 304841 / Rmerge(I) obs: 0.092 / Χ2: 1.62 / D res high: 1.62 Å / D res low: 50 Å / Num. obs: 39739 / % possible obs: 98.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.495099.910.0513.2218.2
2.773.4910010.0662.4148.3
2.422.7710010.0841.6758.4
2.22.4210010.0981.4258.4
2.042.210010.1321.3348.4
1.922.0410010.1971.1998.4
1.821.9210010.3061.148.3
1.751.8299.810.4151.0897.6
1.681.7598.510.51.0976.1
1.621.6885.710.5761.0754.1
ReflectionResolution: 1.62→50 Å / Num. all: 39739 / Num. obs: 39739 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.092 / Χ2: 1.625 / Net I/σ(I): 8.9
Reflection shellResolution: 1.62→1.68 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 2 / Num. unique all: 3434 / Χ2: 1.075 / % possible all: 85.7

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.8 Å / D res low: 48.11 Å / FOM : 0.239 / FOM acentric: 0.249 / FOM centric: 0 / Reflection: 29558 / Reflection acentric: 28375 / Reflection centric: 1183
Phasing MAD setR cullis acentric: 1.91 / R cullis centric: 1 / Highest resolution: 1.8 Å / Lowest resolution: 48.11 Å / Loc acentric: 0.1 / Loc centric: 0 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 28375 / Reflection centric: 1183
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
11.41-48.111.630.20.19726
6.47-11.411.880.20.147562
4.52-6.471.810.20.1116898
3.47-4.521.20.10.12136130
2.82-3.471.390.10.13432167
2.37-2.821.980.105036198
2.05-2.372.78006922231
1.8-2.0511.69009109271
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Br25.034690.8730.9510.3180
2Br39.292360.9320.81-0.0150
3Br29.387941.0850.7360.3190
4Br25.712450.7710.877-0.3770
5Br31.068690.6991.0130.2690
6Br32.645940.4691.1440.0780
7Br24.19150.4261.143-0.0940
8Br28.017291.1390.724-0.0730
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
11.41-48.110.3530.44801239726
6.47-11.410.4190.474053747562
4.52-6.470.4330.46901266116898
3.47-4.520.4080.433022662136130
2.82-3.470.3690.387035993432167
2.37-2.820.2970.309052345036198
2.05-2.370.1980.204071536922231
1.8-2.050.1090.112093809109271

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-3000data collection
RefinementMethod to determine structure: SAD / Resolution: 1.7→38.9 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.712 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1742 5 %RANDOM
Rwork0.175 ---
obs0.177 34926 99.6 %-
all-39739 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.82 Å2 / Biso mean: 24.596 Å2 / Biso min: 6.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0.62 Å2
2---0.17 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 40 475 2938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222552
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9713439
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0965307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54525.504129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61115473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.8621510
X-RAY DIFFRACTIONr_chiral_restr0.0860.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021935
X-RAY DIFFRACTIONr_nbd_refined0.2090.21383
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21758
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2353
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.245
X-RAY DIFFRACTIONr_mcbond_it0.8341.51564
X-RAY DIFFRACTIONr_mcangle_it1.3322460
X-RAY DIFFRACTIONr_scbond_it2.19731118
X-RAY DIFFRACTIONr_scangle_it3.5074.5976
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 122 -
Rwork0.249 2364 -
all-2486 -
obs--95.87 %
Refinement TLS params.Method: refined / Origin x: -5.4697 Å / Origin y: 4.67 Å / Origin z: 12.3334 Å
111213212223313233
T-0.1526 Å20.0008 Å20.0089 Å2--0.1507 Å20.0004 Å2---0.1358 Å2
L0.3234 °20.031 °20.3863 °2-0.2309 °20.1685 °2--1.183 °2
S-0.0002 Å °0.0091 Å °0.0023 Å °-0.0131 Å °-0.013 Å °-0.0073 Å °-0.0416 Å °-0.0071 Å °0.0132 Å °

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