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- PDB-9wuh: Quinoprotein aldose dehydrogenase in PQQ-unbound form -

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Basic information

Entry
Database: PDB / ID: 9wuh
TitleQuinoprotein aldose dehydrogenase in PQQ-unbound form
ComponentsGlucose/Sorbosone dehydrogenase domain-containing protein
KeywordsOXIDOREDUCTASE / Quinoprotein
Function / homologyGlucose/Sorbosone dehydrogenase / Glucose / Sorbosone dehydrogenase / Soluble quinoprotein glucose/sorbosone dehydrogenase / Six-bladed beta-propeller, TolB-like / metal ion binding / Glucose/Sorbosone dehydrogenase domain-containing protein
Function and homology information
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSakuraba, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: to be published
Title: Quinoprotein aldose dehydrogenase in PQQ-unbound form
Authors: Sakuraba, H.
History
DepositionSep 18, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucose/Sorbosone dehydrogenase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3923
Polymers40,2611
Non-polymers1312
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-45 kcal/mol
Surface area13400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.267, 73.267, 150.117
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Glucose/Sorbosone dehydrogenase domain-containing protein / Quinoprotein aldose dehydrogenase


Mass: 40260.914 Da / Num. of mol.: 1 / Mutation: R64Q,D350N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Gene: PAE2689 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZUN8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG600, imidazole buffer, zinc acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→49.02 Å / Num. obs: 28196 / % possible obs: 99 % / Redundancy: 12.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.05 / Rrim(I) all: 0.177 / Χ2: 0.96 / Net I/σ(I): 14.5
Reflection shellResolution: 2→2.05 Å / % possible obs: 89.2 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.98 / Num. measured all: 14537 / Num. unique obs: 1793 / CC1/2: 0.632 / Rpim(I) all: 0.353 / Rrim(I) all: 1.046 / Χ2: 0.92 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→49.02 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22208 1362 -RANDOM
Rwork0.19167 ---
obs0.19318 26769 98.94 %-
Displacement parametersBiso mean: 25.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2--0.94 Å20 Å2
3----1.88 Å2
Refinement stepCycle: LAST / Resolution: 2→49.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2514 0 2 104 2620
LS refinement shellResolution: 2→2.05 Å /
Rfactor% reflection
Rfree0.248 -
Rwork0.264 -
obs-88.14 %

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