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- PDB-5yab: Crystal structure of scyllo-inositol dehydrogenase with L-glucose... -

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Basic information

Entry
Database: PDB / ID: 5yab
TitleCrystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity
ComponentsScyllo-inositol dehydrogenase with L-glucose dehydrogenase activity
KeywordsOXIDOREDUCTASE / Rossman fold / homotetramer / sugar metabolism
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
ACETATE ION / Predicted dehydrogenase
Similarity search - Component
Biological speciesParacoccus laeviglucosivorans Nakamura 2015 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsFukano, K. / Shimizu, T. / Sasaki, Y. / Nakamura, A. / Yajima, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS KAKENHI16H04895 Japan
CitationJournal: PLoS ONE / Year: 2018
Title: Structural basis of L-glucose oxidation by scyllo-inositol dehydrogenase: Implications for a novel enzyme subfamily classification
Authors: Fukano, K. / Ozawa, K. / Kokubu, M. / Shimizu, T. / Ito, S. / Sasaki, Y. / Nakamura, A. / Yajima, S.
History
DepositionAug 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / entity_src_gen
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)165,8438
Polymers165,6074
Non-polymers2364
Water15,349852
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17970 Å2
ΔGint-19 kcal/mol
Surface area46310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.974, 127.453, 137.535
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: 41401.707 Da / Num. of mol.: 4 / Fragment: N72S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus laeviglucosivorans Nakamura 2015 (bacteria)
Gene: lgdA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: K7ZP76
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 852 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12 - 35% PEG3350, 0.1 M sodium acetate, pH 4.8 - 5.4

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 160030 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 24.7
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 4.9 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→28.3 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19184 7983 5 %RANDOM
Rwork0.17658 ---
obs0.17734 151942 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.083 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.75→28.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11183 0 16 852 12051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01911473
X-RAY DIFFRACTIONr_bond_other_d00.0210749
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.93715537
X-RAY DIFFRACTIONr_angle_other_deg3.702324589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.851469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26122.481532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.795151766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.25715120
X-RAY DIFFRACTIONr_chiral_restr0.0780.21641
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113311
X-RAY DIFFRACTIONr_gen_planes_other0.010.022809
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9391.3875886
X-RAY DIFFRACTIONr_mcbond_other0.9371.3875884
X-RAY DIFFRACTIONr_mcangle_it1.5852.0757349
X-RAY DIFFRACTIONr_mcangle_other1.5852.0757350
X-RAY DIFFRACTIONr_scbond_it1.3091.555587
X-RAY DIFFRACTIONr_scbond_other1.3091.555588
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1362.2638189
X-RAY DIFFRACTIONr_long_range_B_refined3.85711.75813739
X-RAY DIFFRACTIONr_long_range_B_other3.79411.50713280
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 541 -
Rwork0.218 10443 -
obs--93.23 %

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