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- PDB-8rg1: Soluble glucose dehydrogenase from acinetobacter calcoaceticus - ... -

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Basic information

Entry
Database: PDB / ID: 8rg1
TitleSoluble glucose dehydrogenase from acinetobacter calcoaceticus - wild type pH8
ComponentsQuinoprotein glucose dehydrogenase B
KeywordsOXIDOREDUCTASE / Wild type / PQQ
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: 1.19 Å
AuthorsLublin, V. / Chavas, L. / Stines-Chaumeil, C. / Kauffmann, B. / Giraud, M.F. / Thompson, A.
Funding support France, 1items
OrganizationGrant numberCountry
Other government France
Citation
Journal: 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.M.G.H. / Thureau, A. / Thompson, A. / Stines-Chaumeil, C.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V.
History
DepositionDec 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)101,56912
Polymers100,5862
Non-polymers98310
Water24,9151383
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, sec-saxs and chromatography support dimer state.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-91 kcal/mol
Surface area32770 Å2
Unit cell
Length a, b, c (Å)60.354, 92.508, 84.711
Angle α, β, γ (deg.)90.000, 105.000, 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: 50293.207 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-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
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1383 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 6000, 100 mM TRIS pH8, 2 mM ZnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.18→50 Å / Num. obs: 199471 / % possible obs: 98.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 12.49 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.5
Reflection shellResolution: 1.19→1.233 Å / Redundancy: 2 % / Rmerge(I) obs: 0.42 / Num. unique obs: 1815 / CC1/2: 0.648 / CC star: 0.887 / Rpim(I) all: 0.42 / Rrim(I) all: 0.59 / % possible all: 6.35

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.19→42.56 Å / SU ML: 0.109 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.971
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1728 2000 1 %
Rwork0.1481 197471 -
obs0.1484 199471 69.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.64 Å2
Refinement stepCycle: LAST / Resolution: 1.19→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7076 0 60 1383 8519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01137317
X-RAY DIFFRACTIONf_angle_d1.08269977
X-RAY DIFFRACTIONf_chiral_restr0.08631079
X-RAY DIFFRACTIONf_plane_restr0.00891328
X-RAY DIFFRACTIONf_dihedral_angle_d6.55761014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.19-1.220.1721110.2341080X-RAY DIFFRACTION5.33
1.22-1.250.2094190.22381899X-RAY DIFFRACTION9.34
1.25-1.290.2956300.22012991X-RAY DIFFRACTION14.66
1.29-1.330.2729580.21525644X-RAY DIFFRACTION27.8
1.33-1.380.2211050.206110335X-RAY DIFFRACTION50.69
1.38-1.430.25351530.199115146X-RAY DIFFRACTION74.47
1.43-1.50.22341920.190718975X-RAY DIFFRACTION93.11
1.5-1.570.19362030.170819987X-RAY DIFFRACTION98.09
1.57-1.670.20812040.153320255X-RAY DIFFRACTION99.23
1.67-1.80.18932040.143120107X-RAY DIFFRACTION98.7
1.8-1.980.17112030.137120036X-RAY DIFFRACTION98.18
1.98-2.270.15082070.130420399X-RAY DIFFRACTION99.64
2.27-2.860.18632030.144520120X-RAY DIFFRACTION98.32
2.86-42.560.14662080.142420497X-RAY DIFFRACTION99.06

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