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- PDB-9w1k: Crystal structure of Aedes aegypti Dopachrome Conversion Enzyme. -

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Basic information

Entry
Database: PDB / ID: 9w1k
TitleCrystal structure of Aedes aegypti Dopachrome Conversion Enzyme.
ComponentsDopachrome conversion enzyme
KeywordsISOMERASE / isomerase Dopachrome Aedes aegypti
Function / homologyMajor royal jelly protein/protein yellow / Major royal jelly protein / Six-bladed beta-propeller, TolB-like / extracellular region / ACETIC ACID / Dopachrome conversion enzyme
Function and homology information
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGuo, Y. / Zhang, L. / Guo, D. / Deng, J. / Li, J. / Han, Q.
Funding support United States, China, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI044399 United States
National Natural Science Foundation of China (NSFC)U22A20363 China
CitationJournal: To Be Published
Title: Crystal structure of Aedes aegypti Dopachrome Conversion Enzyme.
Authors: Guo, Y. / Zhang, L. / Wang, S. / Guo, D. / Deng, J. / Li, J. / Han, Q.
History
DepositionJul 25, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dopachrome conversion enzyme
B: Dopachrome conversion enzyme
C: Dopachrome conversion enzyme
D: Dopachrome conversion enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,59234
Polymers211,7234
Non-polymers5,87030
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12330 Å2
ΔGint-4 kcal/mol
Surface area59540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.760, 105.073, 101.404
Angle α, β, γ (deg.)90.00, 109.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Dopachrome conversion enzyme


Mass: 52930.715 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Natural protein from the mosquito larvae / Source: (natural) Aedes aegypti (yellow fever mosquito) / Plasmid details: Whole body of Larvae / Strain: Liverpool / References: UniProt: Q8T4S2

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Sugars , 8 types, 8 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-2-3/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-Manp]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[LFucpa1-6]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-2-3/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-Manp]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4[LFucpa1-6]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-2-3/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Manp]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-3)-[alpha-L-arabinopyranose-(1-6)]beta-D-mannopyranose-(1-4)-beta-D- ...beta-D-mannopyranose-(1-3)-[alpha-L-arabinopyranose-(1-6)]beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 985.886 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[LArapa1-6]DManpb1-4DManpb1-3[LFucpa1-6]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1a_1-5_2*NCC/3=O][a1122h-1b_1-5][a211h-1a_1-5][a1221m-1a_1-5]/1-2-2-2-3-4/a3-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][a-L-Arap]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: Polysaccharide alpha-L-fucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[alpha-L-fucopyranose-(1- ...alpha-L-fucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-4DGlcpNAcb1-3[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2-2/a3-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{[(4+1)][a-L-Fucp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#7: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Manp]{}}LINUCSPDB-CARE
#8: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Manp]{}}LINUCSPDB-CARE
#9: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-3[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 72 molecules

#10: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Ca
#11: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Formula: C2H4O2
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.1 Å3/Da / Density % sol: 41.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Calcium acetate hydrate 0.1 M Sodium cacodylate trihydrate pH 6.5 18% w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 38871 / % possible obs: 93.1 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.31 / Num. unique obs: 2370 / % possible all: 58.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SCALEPACKdata scaling
HKL-2000data reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→29.9 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.887 / Cross valid method: THROUGHOUT / ESU R Free: 0.482 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25561 1807 5 %RANDOM
Rwork0.20791 ---
obs0.21028 34329 92.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.801 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.9→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12902 0 383 50 13335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01913680
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0381.97418703
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.09951581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46624.006669
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.995152100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6961585
X-RAY DIFFRACTIONr_chiral_restr0.0650.22086
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02110561
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.902→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 75 -
Rwork0.293 1476 -
obs--54.67 %

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