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- PDB-3dzt: AeD7-leukotriene E4 complex -

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Basic information

Entry
Database: PDB / ID: 3dzt
TitleAeD7-leukotriene E4 complex
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
Chem-EAH / Long form salivary protein D7L1
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 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 30, 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 20, 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)35,8727
Polymers35,1181
Non-polymers7546
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.567, 65.307, 52.195
Angle α, β, γ (deg.)90.000, 112.340, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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) / Gene: D7 / Plasmid: VR2001 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P18153

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Non-polymers , 5 types, 356 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EAH / (5S,7E,9E,11Z,14Z)-5-hydroxyicosa-7,9,11,14-tetraenoic acid


Mass: 320.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32O3
#4: 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
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.23 Å3/Da / Density % sol: 44.72 %
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: 22-BM / Wavelength: 0.97902 Å
DetectorType: MAR225 CCD / Detector: CCD / Date: Feb 21, 2008 / Details: Si-111
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97902 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 28456 / Num. obs: 28456 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.069 / Χ2: 1.259
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 10.25 / Num. unique all: 2807 / Χ2: 1.044 / % possible all: 99

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
FFTdifference fourierphasing
RefinementResolution: 1.8→32.65 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.887 / SU B: 4.189 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.125 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1438 5.1 %RANDOM
Rwork0.16 ---
obs0.162 28439 99.37 %-
all-28439 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.51 Å2 / Biso mean: 21.087 Å2 / Biso min: 8.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0.74 Å2
2--0.21 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 50 350 2823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222538
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9753409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8915300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40225.433127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52515467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.6931510
X-RAY DIFFRACTIONr_chiral_restr0.0820.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021923
X-RAY DIFFRACTIONr_nbd_refined0.2040.21274
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21757
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2268
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.222
X-RAY DIFFRACTIONr_mcbond_it0.9021.51539
X-RAY DIFFRACTIONr_mcangle_it1.4122422
X-RAY DIFFRACTIONr_scbond_it2.47231126
X-RAY DIFFRACTIONr_scangle_it3.8724.5985
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 111 -
Rwork0.169 1909 -
all-2020 -
obs--96.88 %
Refinement TLS params.Method: refined / Origin x: -5.7044 Å / Origin y: 3.9958 Å / Origin z: 12.6842 Å
111213212223313233
T-0.0627 Å20.0007 Å20.0153 Å2--0.0633 Å20.0015 Å2---0.0352 Å2
L0.7793 °20.0012 °20.6556 °2-0.446 °20.2303 °2--1.9017 °2
S-0.0045 Å °0.1074 Å °0.0082 Å °-0.0106 Å °-0.0201 Å °0.015 Å °-0.0419 Å °0.1279 Å °0.0247 Å °

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