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- PDB-8ji8: Crystal Structure of Prophenoloxidase PPO6 chimeric mutant (F215E... -

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Basic information

Entry
Database: PDB / ID: 8ji8
TitleCrystal Structure of Prophenoloxidase PPO6 chimeric mutant (F215EASNRAIVD224 to G215DGPDSVVR223) 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: 2.65 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 1, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TK receptor
B: TK receptor
C: TK receptor
D: TK receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,30734
Polymers317,2534
Non-polymers2,05430
Water13,944774
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-17 kcal/mol
Surface area50290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.570, 153.660, 223.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
TK receptor / Prophenoloxidase 6


Mass: 79313.188 Da / Num. of mol.: 4 / Mutation: F215EASNRAIVD224 to G215DGPDSVVR223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: 5564622
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q16G28
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 8 / 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.: 19 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 774 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M imidazole pH7.0, 2% v/v Tacsimate pH7.0, 5% v/v 2-ProOH, 6%-10% v/v PEG 3350,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→47.69 Å / Num. obs: 90756 / % possible obs: 98.6 % / Redundancy: 12.6 % / Biso Wilson estimate: 46.1 Å2 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.066 / Rrim(I) all: 0.173 / Net I/σ(I): 12.2
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3878 / Rpim(I) all: 0.436 / Rrim(I) all: 0.907 / % possible all: 86.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→47.69 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.892 / SU B: 14.547 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26133 4599 5.1 %RANDOM
Rwork0.17585 ---
obs0.18018 86146 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.045 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å2-0 Å20 Å2
2---2.16 Å2-0 Å2
3---3.61 Å2
Refinement stepCycle: 1 / Resolution: 2.65→47.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21657 0 108 774 22539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01222330
X-RAY DIFFRACTIONr_bond_other_d0.0010.01621052
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.66630155
X-RAY DIFFRACTIONr_angle_other_deg0.4661.58348200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.07252623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.1285258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12103781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.23172
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0226958
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025738
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_it3.8254.44310525
X-RAY DIFFRACTIONr_mcbond_other3.8174.44310522
X-RAY DIFFRACTIONr_mcangle_it5.9967.97313135
X-RAY DIFFRACTIONr_mcangle_other5.9967.97413136
X-RAY DIFFRACTIONr_scbond_it5.8444.82411805
X-RAY DIFFRACTIONr_scbond_other5.8434.82311806
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7128.64517021
X-RAY DIFFRACTIONr_long_range_B_refined9.5540.8424645
X-RAY DIFFRACTIONr_long_range_B_other9.54940.8424646
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 284 -
Rwork0.299 5557 -
obs--87 %

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