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- PDB-7u1n: Crystal structure of the Anopheles darlingi AD-118 long form D7 s... -

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Basic information

Entry
Database: PDB / ID: 7u1n
TitleCrystal structure of the Anopheles darlingi AD-118 long form D7 salivary protein
ComponentsLong form D7 salivary protein
KeywordsBLOOD CLOTTING / odorant binding protein family / blood feeding
Function / homologyPheromone/general odorant binding protein superfamily / odorant binding / sensory perception of smell / toxin activity / extracellular space / 2-ETHOXYETHANOL / DI(HYDROXYETHYL)ETHER / Long form salivary protein D7L2
Function and homology information
Biological speciesAnopheles darlingi (American malaria mosquito)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.4 Å
AuthorsAlvarenga, P.H. / Gittis, A.G. / Garboczi, D.N. / Andersen, J.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2022
Title: Functional aspects of evolution in a cluster of salivary protein genes from mosquitoes.
Authors: Alvarenga, P.H. / Dias, D.R. / Xu, X. / Francischetti, I.M.B. / Gittis, A.G. / Arp, G. / Garboczi, D.N. / Ribeiro, J.M.C. / Andersen, J.F.
History
DepositionFeb 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Long form D7 salivary protein
B: Long form D7 salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,84113
Polymers69,7842
Non-polymers1,05711
Water2,270126
1
A: Long form D7 salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3836
Polymers34,8921
Non-polymers4915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Long form D7 salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4597
Polymers34,8921
Non-polymers5676
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.730, 71.600, 71.750
Angle α, β, γ (deg.)90.000, 111.227, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Long form D7 salivary protein


Mass: 34892.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles darlingi (American malaria mosquito)
Production host: Escherichia coli (E. coli) / References: UniProt: B6DDQ8

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Non-polymers , 7 types, 137 molecules

#2: Chemical ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 30%P EG 5000 MME, 0.2 M ammonium sulfate, 0.1M HEPES

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Aug 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.4→29.39 Å / Num. obs: 24809 / % possible obs: 94.1 % / Redundancy: 4.78 % / Biso Wilson estimate: 27.19 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.77
Reflection shellResolution: 2.4→2.46 Å / Rmerge(I) obs: 0.284 / Num. unique obs: 1239 / % possible all: 63.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.4→29.39 Å / SU ML: 0.3149 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 33.713
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2685 1981 8.01 %
Rwork0.2057 22740 -
obs0.2107 24721 94.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.84 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4640 0 67 126 4833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00874806
X-RAY DIFFRACTIONf_angle_d0.9996505
X-RAY DIFFRACTIONf_chiral_restr0.0623690
X-RAY DIFFRACTIONf_plane_restr0.0052850
X-RAY DIFFRACTIONf_dihedral_angle_d17.05931730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.3215880.24761097X-RAY DIFFRACTION63.13
2.46-2.530.32871130.25251270X-RAY DIFFRACTION75.29
2.53-2.60.32551340.25411570X-RAY DIFFRACTION90.49
2.6-2.680.33981490.23311663X-RAY DIFFRACTION97.73
2.68-2.780.30991500.23561688X-RAY DIFFRACTION98.45
2.78-2.890.29151440.24251703X-RAY DIFFRACTION98.72
2.89-3.020.32381530.24521685X-RAY DIFFRACTION98.82
3.02-3.180.34741460.23611710X-RAY DIFFRACTION98.99
3.18-3.380.27111540.22671727X-RAY DIFFRACTION99.47
3.38-3.640.26491520.20731704X-RAY DIFFRACTION99.2
3.64-4.010.24391470.18631727X-RAY DIFFRACTION99.57
4.01-4.590.23931480.1611721X-RAY DIFFRACTION99.68
4.59-5.770.18371470.17521743X-RAY DIFFRACTION99.84
5.77-29.390.23061560.17051732X-RAY DIFFRACTION97.02

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