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

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Basic information

Entry
Database: PDB / ID: 5yap
TitleCrystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity complexed with L-glucono-1,5-lactone
ComponentsScyllo-inositol dehydrogenase with L-glucose dehydrogenase activity
KeywordsOXIDOREDUCTASE / homotetramer / rossman fold / sugar metabolism
Function / homology
Function and homology information


: / 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 ...: / 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
L-glucono-1,5-lactone / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Predicted dehydrogenase
Similarity search - Component
Biological speciesParacoccus laeviglucosivorans Nakamura 2015 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.3Jul 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)168,80311
Polymers165,6074
Non-polymers3,1967
Water15,367853
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21580 Å2
ΔGint-52 kcal/mol
Surface area43970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.571, 121.177, 140.865
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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: 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.: 3 / Source method: obtained synthetically / Formula: C6H10O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 853 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate pH 4.8 - 5.4, 12 - 35% PEG3350

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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: Nov 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 137356 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 18.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 2.3 / % possible all: 99

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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: 1.8→31.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.094 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17045 6847 5 %RANDOM
Rwork0.16255 ---
obs0.16295 130434 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.653 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2--1.03 Å20 Å2
3----0.44 Å2
Refinement stepCycle: 1 / Resolution: 1.8→31.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11118 0 212 853 12183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911615
X-RAY DIFFRACTIONr_bond_other_d0.0060.0210767
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.95715764
X-RAY DIFFRACTIONr_angle_other_deg0.9823.00124642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05651457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42822.467531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.179151747
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.36615120
X-RAY DIFFRACTIONr_chiral_restr0.0820.21674
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113322
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022850
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_it1.1051.7975843
X-RAY DIFFRACTIONr_mcbond_other1.1031.7965842
X-RAY DIFFRACTIONr_mcangle_it1.752.6897295
X-RAY DIFFRACTIONr_mcangle_other1.752.6897296
X-RAY DIFFRACTIONr_scbond_it1.6972.0435772
X-RAY DIFFRACTIONr_scbond_other1.6972.0435772
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7542.9848470
X-RAY DIFFRACTIONr_long_range_B_refined4.65715.6613895
X-RAY DIFFRACTIONr_long_range_B_other4.65715.6613896
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.797→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 497 -
Rwork0.232 9261 -
obs--96.57 %

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