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- PDB-8rfk: Soluble glucose dehydrogenase from acinetobacter calcoaceticus - ... -

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Basic information

Entry
Database: PDB / ID: 8rfk
TitleSoluble glucose dehydrogenase from acinetobacter calcoaceticus - single mutant pH8
ComponentsQuinoprotein glucose dehydrogenase B
KeywordsOXIDOREDUCTASE / Double point mutation
Function / homology
Function and homology information


glucose 1-dehydrogenase (PQQ, quinone) / quinoprotein glucose dehydrogenase activity / metal ion binding
Similarity search - Function
PQQ-dependent dehydrogenase, s-GDH family / Glucose/Sorbosone dehydrogenase / Glucose / Sorbosone dehydrogenase / Soluble quinoprotein glucose/sorbosone dehydrogenase / Six-bladed beta-propeller, TolB-like
Similarity search - Domain/homology
: / Quinoprotein glucose dehydrogenase B
Similarity search - Component
Biological speciesAcinetobacter calcoaceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsLublin, V. / Chavas, L. / Stines-Chaumeil, C. / Kauffmann, B. / Giraud, M.F. / Thompson, A.
Funding support France, 1items
OrganizationGrant numberCountry
Other government France
CitationJournal: Biosci.Rep. / Year: 2024
Title: Does Acinetobacter calcoaceticus glucose dehydrogenase produce self-damaging H2O2?
Authors: Lublin, V. / Kauffmann, B. / Engilberge, S. / Durola, F. / Gounel, S. / Bichon, S. / Jean, C. / Mano, N. / Giraud, M.F. / Chavas, L. / Thureau, A. / Thompson, A. / Stines-Chaumeil, C.
History
DepositionDec 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Quinoprotein glucose dehydrogenase B
B: Quinoprotein glucose dehydrogenase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,52310
Polymers100,5542
Non-polymers9698
Water23,4201300
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-82 kcal/mol
Surface area33920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.733, 92.614, 85.341
Angle α, β, γ (deg.)90.000, 105.240, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Quinoprotein glucose dehydrogenase B


Mass: 50277.207 Da / Num. of mol.: 2 / Mutation: D143E,Y343F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter calcoaceticus (bacteria) / Gene: gdhB / Production host: Escherichia coli (E. coli) / References: UniProt: P13650
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-A1H0D / 3-(3,5-dicarboxy-1~{H}-pyrrol-2-yl)pyridine-2,4,6-tricarboxylic acid / PYRROLOQUINOLINE QUINONE [CHARGED]


Mass: 364.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H8N2O10 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1300 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 6000, TRIS, Lithium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.54→46.5 Å / Num. obs: 131392 / % possible obs: 97.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 16.41 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.132 / Net I/σ(I): 10.7
Reflection shellResolution: 1.54→1.63 Å / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 0.58 / Num. unique obs: 18670 / CC1/2: 0.36 / Rrim(I) all: 1.59 / % possible all: 86

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→42.73 Å / SU ML: 0.1354 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.8244
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1854 1999 1.92 %
Rwork0.1584 102214 -
obs0.1589 104213 80.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.61 Å2
Refinement stepCycle: LAST / Resolution: 1.56→42.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7074 0 58 1300 8432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00477325
X-RAY DIFFRACTIONf_angle_d0.79929989
X-RAY DIFFRACTIONf_chiral_restr0.05321082
X-RAY DIFFRACTIONf_plane_restr0.00711330
X-RAY DIFFRACTIONf_dihedral_angle_d6.36671014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.20750.2726234X-RAY DIFFRACTION2.6
1.6-1.640.2582330.25931709X-RAY DIFFRACTION18.84
1.64-1.690.3004730.25833726X-RAY DIFFRACTION40.99
1.69-1.740.33251280.27316503X-RAY DIFFRACTION71.62
1.74-1.80.27441600.24878220X-RAY DIFFRACTION90.77
1.8-1.880.24211730.23748897X-RAY DIFFRACTION98.02
1.88-1.960.2171790.20429107X-RAY DIFFRACTION99.81
1.96-2.070.18271770.16889086X-RAY DIFFRACTION99.9
2.07-2.190.18191780.1559056X-RAY DIFFRACTION99.73
2.19-2.360.19731770.15029068X-RAY DIFFRACTION99.46
2.36-2.60.16931770.15059075X-RAY DIFFRACTION99.73
2.6-2.980.19411790.14739108X-RAY DIFFRACTION99.82
2.98-3.750.17191780.13569155X-RAY DIFFRACTION99.89
3.75-42.730.13951820.1269270X-RAY DIFFRACTION99.87

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