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- PDB-9x6n: Crystal structure of Klebsiella oxytoca ribitol dehydrogenase in ... -

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Basic information

Entry
Database: PDB / ID: 9x6n
TitleCrystal structure of Klebsiella oxytoca ribitol dehydrogenase in complex with D-allulose
ComponentsRibitol 2-dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold / dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / D-psicose / alpha-D-psicofuranose / alpha-D-psicopyranose / Ribitol 2-dehydrogenase
Similarity search - Component
Biological speciesKlebsiella oxytoca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsYoshida, H. / Yoshihara, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)25K08924 Japan
CitationJournal: Febs Lett. / Year: 2026
Title: Crystal structures of Klebsiella oxytoca ribitol dehydrogenase in complex with NAD + , d-allose, or d-allulose reveal insight into substrate recognition.
Authors: Yoshida, H. / Matsumoto, M. / Yamamoto, N. / Yoshihara, A. / Izumori, K. / Kamitori, S.
History
DepositionOct 15, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribitol 2-dehydrogenase
B: Ribitol 2-dehydrogenase
C: Ribitol 2-dehydrogenase
D: Ribitol 2-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,91211
Polymers114,1314
Non-polymers7817
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13870 Å2
ΔGint-18 kcal/mol
Surface area36510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.008, 102.869, 80.574
Angle α, β, γ (deg.)90.00, 109.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Ribitol 2-dehydrogenase


Mass: 28532.748 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: This is a His-tagged recombinant protein containing 21 residues (MGSSHHHHHHSSGLVPRGSHS ) at the N-terminus. Some residues are missing their side chains due to unclear electron density maps. ...Details: This is a His-tagged recombinant protein containing 21 residues (MGSSHHHHHHSSGLVPRGSHS ) at the N-terminus. Some residues are missing their side chains due to unclear electron density maps. They are refined as Ala or Gly but not mutated.
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: DET57_113163 / Plasmid: plasmid / Details (production host): pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A318FHD8

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Sugars , 2 types, 2 molecules

#4: Sugar ChemComp-PSJ / D-psicose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Sugar ChemComp-PSV / alpha-D-psicofuranose / alpha-D-psicose / D-psicose / psicose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DPsifaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-psicofuranoseCOMMON NAMEGMML 1.0
a-D-PsifIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
PsiSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 459 molecules

#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O
#3: Chemical ChemComp-WEB / alpha-D-psicopyranose / (2~{S},3~{R},4~{R},5~{R})-2-(hydroxymethyl)oxane-2,3,4,5-tetrol


Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: ammonium sulfate, isopropanol, PEG8000, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→42.61 Å / Num. obs: 138604 / % possible obs: 99.5 % / Redundancy: 3.3 % / CC1/2: 1 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.022 / Rrim(I) all: 0.041 / Χ2: 1.04 / Net I/σ(I): 20.1
Reflection shellResolution: 1.56→1.59 Å / % possible obs: 99.3 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.512 / Num. measured all: 20017 / Num. unique obs: 6796 / CC1/2: 0.77 / Rpim(I) all: 0.354 / Rrim(I) all: 0.625 / Χ2: 0.9 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→42.61 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.689 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19226 6779 4.9 %RANDOM
Rwork0.16867 ---
obs0.16982 131793 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.743 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.56→42.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7405 0 52 454 7911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0137592
X-RAY DIFFRACTIONr_bond_other_d00.0177351
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.62610341
X-RAY DIFFRACTIONr_angle_other_deg1.3581.57516978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.26251009
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93922.985325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.203151226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2031539
X-RAY DIFFRACTIONr_chiral_restr0.060.21038
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028562
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021443
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_it3.2222.2484024
X-RAY DIFFRACTIONr_mcbond_other3.2222.2484023
X-RAY DIFFRACTIONr_mcangle_it4.1413.3625025
X-RAY DIFFRACTIONr_mcangle_other4.1413.3625026
X-RAY DIFFRACTIONr_scbond_it4.4672.63568
X-RAY DIFFRACTIONr_scbond_other4.4662.63569
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0533.7285313
X-RAY DIFFRACTIONr_long_range_B_refined7.12228.2688275
X-RAY DIFFRACTIONr_long_range_B_other7.1328.1718204
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.56→1.601 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 535 -
Rwork0.273 9674 -
obs--99.42 %

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