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- PDB-6ktk: Crystal structure of scyllo-inositol dehydrogenase R178A mutant, ... -

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Basic information

Entry
Database: PDB / ID: 6ktk
TitleCrystal structure of scyllo-inositol dehydrogenase R178A mutant, complexed with NADH and L-glucono-1,5-lactone, from Paracoccus laeviglucosivorans
ComponentsScyllo-inositol dehydrogenase with L-glucose dehydrogenase activity
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich ...Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-glucono-1,5-lactone / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Predicted dehydrogenase
Similarity search - Component
Biological speciesParacoccus laeviglucosivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSuzuki, M. / Koubara, K. / Takenoya, M. / Fukano, K. / Ito, S. / Sasaki, Y. / Nakamura, A. / Yajima, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16H04895 Japan
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2020
Title: Single amino acid mutation altered substrate specificity for L-glucose and inositol inscyllo-inositol dehydrogenase isolated fromParacoccus laeviglucosivorans.
Authors: Suzuki, M. / Koubara, K. / Takenoya, M. / Fukano, K. / Ito, S. / Sasaki, Y. / Nakamura, A. / Yajima, S.
History
DepositionAug 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity
B: Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity
C: Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity
D: Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,02514
Polymers165,2624
Non-polymers3,76310
Water16,754930
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21630 Å2
ΔGint-52 kcal/mol
Surface area45750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.610, 127.560, 137.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity


Mass: 41315.594 Da / Num. of mol.: 4 / Mutation: R178A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus laeviglucosivorans (bacteria)
Gene: lgdA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K7ZP76
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Sugar
ChemComp-8S0 / L-glucono-1,5-lactone / (3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-one


Type: L-saccharide / Mass: 178.140 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H10O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 930 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsunintended mutation

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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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium acetate, pH 5.2, and 20% PEG3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 190486 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.9
Reflection shellResolution: 1.65→1.69 Å / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 13395 / CC1/2: 0.898

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5yab

5yab


Resolution: 1.65→48.4 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.171 9602 5 %
Rwork0.16 --
obs0.16 180883 99.6 %
Refinement stepCycle: LAST / Resolution: 1.65→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11159 0 250 930 12339
LS refinement shellResolution: 1.65→1.69 Å
RfactorNum. reflection% reflection
Rfree0.218 701 5 %
Rwork0.213 12679 -
obs--95.7 %

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