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- PDB-8yav: Crystal structure of glucose 1-dehydrogenase from Limosilactobaci... -

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Basic information

Entry
Database: PDB / ID: 8yav
TitleCrystal structure of glucose 1-dehydrogenase from Limosilactobacillus fermentum
ComponentsSDR family oxidoreductase
KeywordsHYDROLASE / glucose 1-dehydrogenase
Function / homologyPKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / SDR family oxidoreductase
Function and homology information
Biological speciesLimosilactobacillus fermentum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsCong, L. / Wang, J.J. / Wei, H.L. / Liu, W.D. / You, S.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Scholarship Council China
CitationJournal: Adv.Synth.Catal. / Year: 2024
Title: Structure-Guided Engineering of a Short-Chain Dehydrogenase LfSDR1 for Efficient Biosynthesis of (R)-9-(2-Hydroxypropyl)adenine, the Key Intermediate of Tenofovir.
Authors: Wang, Q. / Cong, L. / Guo, J. / Wang, J. / Han, X. / Zhang, W. / Liu, W. / Wei, H. / You, S.
History
DepositionFeb 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SDR family oxidoreductase
B: SDR family oxidoreductase
C: SDR family oxidoreductase
D: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,3406
Polymers105,2924
Non-polymers492
Water10,052558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12820 Å2
ΔGint-106 kcal/mol
Surface area33300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.851, 58.079, 73.072
Angle α, β, γ (deg.)70.580, 83.460, 78.360
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
SDR family oxidoreductase


Mass: 26322.930 Da / Num. of mol.: 4 / Mutation: G146D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limosilactobacillus fermentum (bacteria)
Gene: GC247_10055 / Plasmid: pET-32a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A843R2C6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M MES pH 6.0, 0.05M CaCl2, 43% PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 1, 2022
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→42.97 Å / Num. obs: 85496 / % possible obs: 96.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 20.25 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.083 / Net I/σ(I): 14
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 3 / Num. unique obs: 4143 / CC1/2: 0.855 / % possible all: 89.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7P7Y

7p7y


Resolution: 1.75→42.97 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0.46 / Phase error: 23.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2167 1997 2.34 %
Rwork0.1891 83470 -
obs0.1898 85467 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.98 Å2 / Biso mean: 24.5888 Å2 / Biso min: 7.64 Å2
Refinement stepCycle: final / Resolution: 1.75→42.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7356 0 2 558 7916
Biso mean--16.63 33.08 -
Num. residues----984
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.810.34671970.33667889808692
1.81-1.890.34141810.25558319850096
1.89-1.970.26591980.21358311850996
1.97-2.080.22062030.20338309851296
2.08-2.210.23522020.20298374857697
2.21-2.380.22742000.19318366856697
2.38-2.610.24012060.18998424863097
2.61-2.990.21322010.18698439864098
2.99-3.770.19482010.16688510871198
3.77-42.970.17312080.1658529873799

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