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

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Basic information

Entry
Database: PDB / ID: 5yaq
TitleCrystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity complexed with scyllo-inosose
ComponentsScyllo-inositol dehydrogenase with L-glucose dehydrogenase activity
KeywordsOXIDOREDUCTASE / Rossman fold / homotetramer / sugar metabolism
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
: / : / GFO/IDH/MocA C-terminal domain / 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 ...: / : / GFO/IDH/MocA C-terminal domain / 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
Chem-ISE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Predicted dehydrogenase
Similarity search - Component
Biological speciesParacoccus laeviglucosivorans Nakamura 2015 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsFukano, K. / Shimizu, T. / Sasaki, Y. / Nakamura, A. / Yajima, S.
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
DepositionSep 1, 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 1.3Nov 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 / refine_hist
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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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)168,79511
Polymers165,6074
Non-polymers3,1887
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21540 Å2
ΔGint-52 kcal/mol
Surface area43820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.550, 121.243, 140.395
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 / Mutation: 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-ISE / (2R,3S,4s,5R,6S)-2,3,4,5,6-pentahydroxycyclohexanone / Inosose / Myo-inosose


Mass: 178.140 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H10O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.22 Å3/Da / Density % sol: 44.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate pH 4.8 - 5.4, and 12 - 35% PEG3350

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 100761 / % possible obs: 99.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 22.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 3.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YAB

5yab


Resolution: 1.99→39 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.18 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19352 5054 5 %RANDOM
Rwork0.18006 ---
obs0.18073 95631 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.305 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20 Å2
2--1.37 Å20 Å2
3----0.86 Å2
Refinement stepCycle: 1 / Resolution: 1.99→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11110 0 212 465 11787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911607
X-RAY DIFFRACTIONr_bond_other_d0.0070.0210764
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.95815756
X-RAY DIFFRACTIONr_angle_other_deg1.001324614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48551456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69722.467531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.679151745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8915120
X-RAY DIFFRACTIONr_chiral_restr0.0860.21675
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113315
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022853
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_it1.0912.2035839
X-RAY DIFFRACTIONr_mcbond_other1.092.2035838
X-RAY DIFFRACTIONr_mcangle_it1.6833.2997290
X-RAY DIFFRACTIONr_mcangle_other1.6833.2997291
X-RAY DIFFRACTIONr_scbond_it1.4572.445768
X-RAY DIFFRACTIONr_scbond_other1.4572.445769
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3033.5968467
X-RAY DIFFRACTIONr_long_range_B_refined3.59118.48913351
X-RAY DIFFRACTIONr_long_range_B_other3.59118.48913351
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.994→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 342 -
Rwork0.223 6758 -
obs--95.86 %

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