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- PDB-8re0: Soluble glucose dehydrogenase from acinetobacter calcoaceticus - ... -

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Basic information

Entry
Database: PDB / ID: 8re0
TitleSoluble glucose dehydrogenase from acinetobacter calcoaceticus - double 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 9, 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)101,53011
Polymers100,5542
Non-polymers9769
Water23,8341323
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-87 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
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: Chemical ChemComp-LI / LITHIUM ION / Lithium


Mass: 6.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Li
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1323 / 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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG 6000, 100mM TRIS pH8, 200 mM LiCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.976 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: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.56→43 Å / Num. obs: 104245 / % possible obs: 81.54 % / Redundancy: 2 % / Biso Wilson estimate: 16.41 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.077 / Net I/σ(I): 12.89
Reflection shellResolution: 1.566→1.622 Å / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 1089 / CC1/2: 0.468 / CC star: 0.799 / Rrim(I) all: 0.659 / % possible all: 8.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→42.73 Å / SU ML: 0.1467 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.7464
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1835 5201 4.99 %
Rwork0.1601 99024 -
obs0.1613 104225 80.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.51 Å2
Refinement stepCycle: LAST / Resolution: 1.56→42.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7074 0 59 1323 8456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00967325
X-RAY DIFFRACTIONf_angle_d0.96219989
X-RAY DIFFRACTIONf_chiral_restr0.06531082
X-RAY DIFFRACTIONf_plane_restr0.00871330
X-RAY DIFFRACTIONf_dihedral_angle_d6.42031014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.570.707810.257230X-RAY DIFFRACTION0.73
1.58-1.590.152740.2524162X-RAY DIFFRACTION3.88
1.59-1.610.4003150.2707496X-RAY DIFFRACTION11.94
1.61-1.630.3066530.2492869X-RAY DIFFRACTION21.23
1.63-1.650.2475830.24041299X-RAY DIFFRACTION31.95
1.65-1.680.2921060.25851732X-RAY DIFFRACTION42.56
1.68-1.70.28031200.28142259X-RAY DIFFRACTION55.51
1.7-1.730.30941650.28292947X-RAY DIFFRACTION71.77
1.73-1.750.25421840.26283497X-RAY DIFFRACTION85.17
1.75-1.780.27271820.25443740X-RAY DIFFRACTION90.02
1.78-1.810.24511840.23623834X-RAY DIFFRACTION94.14
1.81-1.850.26192080.23434044X-RAY DIFFRACTION97.7
1.85-1.880.26712310.23954056X-RAY DIFFRACTION99.51
1.88-1.920.2582250.21494043X-RAY DIFFRACTION99.84
1.92-1.960.21072000.1884188X-RAY DIFFRACTION99.86
1.96-2.010.20842140.17554067X-RAY DIFFRACTION99.93
2.01-2.060.18171830.16534159X-RAY DIFFRACTION99.93
2.06-2.110.1752360.15454069X-RAY DIFFRACTION99.84
2.11-2.180.19862140.15254111X-RAY DIFFRACTION99.7
2.18-2.250.18991990.15124130X-RAY DIFFRACTION99.36
2.25-2.330.17792100.15074102X-RAY DIFFRACTION99.52
2.33-2.420.17982180.14624073X-RAY DIFFRACTION99.58
2.42-2.530.18512320.14884135X-RAY DIFFRACTION99.79
2.53-2.660.19352330.15084073X-RAY DIFFRACTION99.81
2.66-2.830.16822350.14924098X-RAY DIFFRACTION99.86
2.83-3.050.15752160.15364154X-RAY DIFFRACTION99.84
3.05-3.350.18031860.14784138X-RAY DIFFRACTION99.84
3.35-3.840.14772460.13084119X-RAY DIFFRACTION99.98
3.84-4.840.13312120.11354157X-RAY DIFFRACTION99.84
4.84-42.730.15032060.15064243X-RAY DIFFRACTION99.89

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