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- PDB-9wui: Quinoprotein aldose dehydrogenase in PQQ-bound form -

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Basic information

Entry
Database: PDB / ID: 9wui
TitleQuinoprotein aldose dehydrogenase in PQQ-bound 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 / PYRROLOQUINOLINE QUINONE / Glucose/Sorbosone dehydrogenase domain-containing protein
Function and homology information
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSakuraba, H. / Yoneda, K.
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-bound form
Authors: Sakuraba, H. / Yoneda, K.
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)40,8026
Polymers40,2611
Non-polymers5415
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-33 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.544, 73.544, 150.236
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-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H6N2O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.52 Å3/Da / Density % sol: 51.25 %
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: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Mar 8, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→49.19 Å / Num. obs: 30959 / % possible obs: 100 % / Redundancy: 25.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.236 / Rpim(I) all: 0.048 / Rrim(I) all: 0.241 / Χ2: 0.98 / Net I/σ(I): 16.9
Reflection shellResolution: 1.95→2 Å / % possible obs: 100 % / Redundancy: 21 % / Rmerge(I) obs: 1.57 / Num. measured all: 44579 / Num. unique obs: 2122 / CC1/2: 0.736 / Rpim(I) all: 0.348 / Rrim(I) all: 1.609 / Χ2: 0.96 / Net I/σ(I) obs: 2.7

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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: 1.95→49.19 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21108 1622 -RANDOM
Rwork0.18182 ---
obs0.18332 29264 99.99 %-
Displacement parametersBiso mean: 26.919 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2--1.1 Å20 Å2
3----2.19 Å2
Refinement stepCycle: LAST / Resolution: 1.95→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2550 0 28 115 2693
LS refinement shellResolution: 1.95→2 Å /
Rfactor% reflection
Rfree0.281 -
Rwork0.287 -
obs-100 %

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