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- PDB-8jib: Crystal Structure of Prophenoloxidase PPO6 from Aedes aegypti -

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Basic information

Entry
Database: PDB / ID: 8jib
TitleCrystal Structure of Prophenoloxidase PPO6 from Aedes aegypti
ComponentsTK receptor
KeywordsIMMUNE SYSTEM / Prophenoloxidase.
Function / homology
Function and homology information


melanotic encapsulation of foreign target / tyrosinase / catechol oxidase activity / tyrosinase activity / melanin biosynthetic process / dopamine metabolic process / extracellular region / metal ion binding
Similarity search - Function
Arthropod hemocyanins / insect LSPs signature 1. / Arthropod hemocyanins / insect LSPs signature 2. / Hemocyanin, N-terminal / Hemocyanin, N-terminal domain superfamily / Hemocyanin, all-alpha domain / Hemocyanin/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, C-terminal domain superfamily / Hemocyanin, copper containing domain / Hemocyanin, ig-like domain ...Arthropod hemocyanins / insect LSPs signature 1. / Arthropod hemocyanins / insect LSPs signature 2. / Hemocyanin, N-terminal / Hemocyanin, N-terminal domain superfamily / Hemocyanin, all-alpha domain / Hemocyanin/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, C-terminal domain superfamily / Hemocyanin, copper containing domain / Hemocyanin, ig-like domain / Hemocyanin/hexamerin / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily / Immunoglobulin E-set
Similarity search - Domain/homology
COPPER (II) ION / tyrosinase
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsZhu, X. / Zhang, L. / Yang, X. / Bao, P. / Ren, D. / Han, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31860702 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: The Aedes aegypti mosquito evolves two types of prophenoloxidases with diversified functions.
Authors: Zhu, X. / Zhang, L. / Jiang, L. / Chen, H. / Tang, Y. / Yang, X. / Bao, P. / Liao, C. / Li, J. / Vavricka, C.J. / Ren, D. / Chen, Z. / Guo, Y. / Han, Q.
History
DepositionMay 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Apr 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TK receptor
B: TK receptor
C: TK receptor
D: TK receptor
E: TK receptor
F: TK receptor
G: TK receptor
H: TK receptor
I: TK receptor
J: TK receptor
K: TK receptor
L: TK receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)956,36143
Polymers954,40112
Non-polymers1,96031
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-73 kcal/mol
Surface area50560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.041, 364.149, 125.522
Angle α, β, γ (deg.)90.00, 118.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
TK receptor


Mass: 79533.453 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: 5564622 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16G28
#2: Chemical...
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M MgCl2,0.1 M Sodium Cacodylate pH6.5,10%-15% v/v PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.15→48.66 Å / Num. obs: 161746 / % possible obs: 98.8 % / Redundancy: 3.8 % / CC1/2: 0.967 / Rmerge(I) obs: 0.241 / Rpim(I) all: 0.135 / Rrim(I) all: 0.278 / Rsym value: 0.241 / Net I/σ(I): 5
Reflection shellResolution: 3.15→3.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 23632 / CC1/2: 0.429 / Rpim(I) all: 0.499 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→48.66 Å / Cor.coef. Fo:Fc: 0.839 / Cor.coef. Fo:Fc free: 0.786 / SU B: 41.416 / Cross valid method: THROUGHOUT / ESU R Free: 0.649 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31041 7921 4.9 %RANDOM
Rwork0.26932 ---
obs0.27134 153764 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.886 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20.62 Å2
2---1.08 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: 1 / Resolution: 3.15→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms64944 0 52 165 65161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01266672
X-RAY DIFFRACTIONr_bond_other_d0.0010.01662732
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.83890132
X-RAY DIFFRACTIONr_angle_other_deg0.4951.781143617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33857834
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.8265767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.1781011352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.29505
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0280719
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0217237
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7786.62431444
X-RAY DIFFRACTIONr_mcbond_other4.7786.62431444
X-RAY DIFFRACTIONr_mcangle_it8.03711.91339242
X-RAY DIFFRACTIONr_mcangle_other8.03711.91339243
X-RAY DIFFRACTIONr_scbond_it4.1776.79135228
X-RAY DIFFRACTIONr_scbond_other4.1776.79135229
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.18312.450891
X-RAY DIFFRACTIONr_long_range_B_refined12.41766.5273364
X-RAY DIFFRACTIONr_long_range_B_other12.41766.5273364
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.15→3.228 Å
RfactorNum. reflection% reflection
Rfree0.388 441 -
Rwork0.362 11376 -
obs--97.91 %

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