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- PDB-9x6l: Crystal structure of Klebsiella oxytoca ribitol dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 9x6l
TitleCrystal structure of Klebsiella oxytoca ribitol dehydrogenase
ComponentsRibitol 2-dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold / dehydrogenase
Function / homologyshort chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / Ribitol 2-dehydrogenase
Function and homology information
Biological speciesKlebsiella oxytoca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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)114,62812
Polymers114,1314
Non-polymers4978
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14320 Å2
ΔGint-11 kcal/mol
Surface area35900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.049, 102.658, 80.984
Angle α, β, γ (deg.)90.00, 109.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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.
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: DET57_113163 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A318FHD8
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 43.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: lithium sulfate, PEG3350, Tris

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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: Nov 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→42.6 Å / Num. obs: 69343 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.059 / Rrim(I) all: 0.109 / Χ2: 1.06 / Net I/σ(I): 9
Reflection shellResolution: 1.97→2.01 Å / % possible obs: 99.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.608 / Num. measured all: 14739 / Num. unique obs: 4540 / CC1/2: 0.695 / Rpim(I) all: 0.401 / Rrim(I) all: 0.731 / Χ2: 1.1 / Net I/σ(I) obs: 2.1

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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: 1.97→42.6 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.301 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22373 3419 4.9 %RANDOM
Rwork0.18416 ---
obs0.18611 65898 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.906 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.97→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7296 0 32 186 7514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137435
X-RAY DIFFRACTIONr_bond_other_d00.0177242
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.62110108
X-RAY DIFFRACTIONr_angle_other_deg1.3121.56916717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1875981
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43123.123317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.211151208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5671537
X-RAY DIFFRACTIONr_chiral_restr0.0650.21010
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028357
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021406
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_it2.7322.7393942
X-RAY DIFFRACTIONr_mcbond_other2.7322.7393941
X-RAY DIFFRACTIONr_mcangle_it3.6824.094917
X-RAY DIFFRACTIONr_mcangle_other3.6824.094918
X-RAY DIFFRACTIONr_scbond_it3.3163.0433493
X-RAY DIFFRACTIONr_scbond_other3.3153.0433494
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8394.4265192
X-RAY DIFFRACTIONr_long_range_B_refined5.88233.1247940
X-RAY DIFFRACTIONr_long_range_B_other5.88333.1157914
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 265 -
Rwork0.272 4878 -
obs--100 %

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