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- PDB-9x6m: Crystal structure of Klebsiella oxytoca ribitol dehydrogenase in ... -

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Basic information

Entry
Database: PDB / ID: 9x6m
TitleCrystal structure of Klebsiella oxytoca ribitol dehydrogenase in complex with D-allose
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 / beta-D-allopyranose / Ribitol 2-dehydrogenase
Function and homology information
Biological speciesKlebsiella oxytoca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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)114,6717
Polymers114,1314
Non-polymers5403
Water12,052669
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13730 Å2
ΔGint-44 kcal/mol
Surface area34880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.184, 102.899, 81.488
Angle α, β, γ (deg.)90.00, 110.14, 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. A few 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. A few residues are missing their side chains due to unclear electron density maps. They are refined as Ala but not mutated.
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: DET57_113163 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A318FHD8
#2: Sugar ChemComp-ALL / beta-D-allopyranose / beta-D-allose / D-allose / allose / D-ALLOPYRANOSE


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DAllpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-allopyranoseCOMMON NAMEGMML 1.0
b-D-AllpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AllSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / Source method: isolated from a natural source / Formula: H2O
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: 2.21 Å3/Da / Density % sol: 44.43 %
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: May 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→42.73 Å / Num. obs: 102862 / % possible obs: 99.4 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.04 / Rrim(I) all: 0.074 / Χ2: 1.05 / Net I/σ(I): 12.3
Reflection shellResolution: 1.73→1.76 Å / % possible obs: 98.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.624 / Num. measured all: 16122 / Num. unique obs: 5027 / CC1/2: 0.695 / Rpim(I) all: 0.411 / Rrim(I) all: 0.75 / Χ2: 0.97 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→40.972 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1921 5076 4.95 %RANDOM
Rwork0.1596 ---
obs0.1612 102608 99.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→40.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7119 0 36 669 7824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057276
X-RAY DIFFRACTIONf_angle_d0.7789915
X-RAY DIFFRACTIONf_dihedral_angle_d5.6445504
X-RAY DIFFRACTIONf_chiral_restr0.0521227
X-RAY DIFFRACTIONf_plane_restr0.0051274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.74970.2881560.24873180X-RAY DIFFRACTION98
1.7497-1.77020.26331780.23483224X-RAY DIFFRACTION98
1.7702-1.79180.28571840.21223153X-RAY DIFFRACTION98
1.7918-1.81450.22291700.20863212X-RAY DIFFRACTION98
1.8145-1.83840.26061830.2163213X-RAY DIFFRACTION98
1.8384-1.86360.25451760.19733196X-RAY DIFFRACTION99
1.8636-1.89020.21131840.18593278X-RAY DIFFRACTION99
1.8902-1.91840.21281910.18073152X-RAY DIFFRACTION99
1.9184-1.94840.24191790.17633244X-RAY DIFFRACTION99
1.9484-1.98030.20171810.17613228X-RAY DIFFRACTION99
1.9803-2.01450.20512110.16163202X-RAY DIFFRACTION99
2.0145-2.05110.1981550.15623272X-RAY DIFFRACTION99
2.0511-2.09060.21021610.1583241X-RAY DIFFRACTION99
2.0906-2.13320.19271530.15313248X-RAY DIFFRACTION99
2.1332-2.17960.18381580.14813263X-RAY DIFFRACTION99
2.1796-2.23030.18481500.14513269X-RAY DIFFRACTION99
2.2303-2.28610.19961830.14613243X-RAY DIFFRACTION99
2.2861-2.34790.17471590.14653260X-RAY DIFFRACTION99
2.3479-2.4170.17141660.14273247X-RAY DIFFRACTION99
2.417-2.4950.2031580.14833297X-RAY DIFFRACTION100
2.495-2.58410.2211680.15513249X-RAY DIFFRACTION100
2.5841-2.68760.17751530.15953303X-RAY DIFFRACTION100
2.6876-2.80990.18881290.15743330X-RAY DIFFRACTION100
2.8099-2.9580.20411490.15413280X-RAY DIFFRACTION100
2.958-3.14320.20881800.16313280X-RAY DIFFRACTION100
3.1432-3.38580.1831940.16243262X-RAY DIFFRACTION100
3.3858-3.72630.17491510.14813289X-RAY DIFFRACTION100
3.7263-4.26510.17051670.13713304X-RAY DIFFRACTION99
4.2651-5.37160.15121660.13543295X-RAY DIFFRACTION100
5.3716-40.9720.1681830.1813318X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.67840.19650.06630.8151-0.2550.78330.00940.0838-0.1014-0.11880.02820.06890.1197-0.0557-0.03360.1853-0.0092-0.00430.1999-0.02590.183812.429639.023420.5556
20.6560.1919-0.08140.8227-0.07640.5818-0.04830.17180.1407-0.20060.0650.1946-0.0298-0.0612-0.01560.2181-0.0037-0.03720.27420.04590.207612.800668.08775.2302
30.5992-0.03420.10360.97370.07780.4185-0.03890.1590.1182-0.1240.0063-0.1028-0.0560.10630.02940.1662-0.01540.02320.21290.02940.198238.713475.067318.0828
40.6727-0.04240.15730.5868-0.23550.44550.0102-0.0221-0.0710.0302-0.0181-0.04420.0190.02790.00940.15040.01450.00870.171-0.02260.170736.451845.84935.8407
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 23 through 270)
2X-RAY DIFFRACTION2(chain 'B' and resid 30 through 270)
3X-RAY DIFFRACTION3(chain 'C' and resid 11 through 270)
4X-RAY DIFFRACTION4(chain 'D' and resid 10 through 270)

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