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- PDB-9x6o: Crystal structure of Klebsiella oxytoca ribitol dehydrogenase in ... -

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Basic information

Entry
Database: PDB / ID: 9x6o
TitleCrystal structure of Klebsiella oxytoca ribitol dehydrogenase in complex with NAD+
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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Ribitol 2-dehydrogenase
Function and homology information
Biological speciesKlebsiella oxytoca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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)111,6438
Polymers108,9894
Non-polymers2,6544
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16390 Å2
ΔGint-83 kcal/mol
Surface area32700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.399, 61.509, 70.873
Angle α, β, γ (deg.)113.71, 92.14, 109.32
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Ribitol 2-dehydrogenase


Mass: 27247.312 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: This is a His-tagged recombinant protein containing 8 residues (GSHHHHHH ) at the C-terminus.
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: DET57_113163 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: A0A318FHD8
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: calcium acetate, PEG400, acetate, NAD+

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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 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→48.7 Å / Num. obs: 68325 / % possible obs: 97.1 % / Redundancy: 3.5 % / CC1/2: 1 / Rmerge(I) obs: 0.027 / Rpim(I) all: 0.017 / Rrim(I) all: 0.032 / Χ2: 1.08 / Net I/σ(I): 22.6
Reflection shellResolution: 1.89→1.93 Å / % possible obs: 96.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.52 / Num. measured all: 15999 / Num. unique obs: 4420 / CC1/2: 0.865 / Rpim(I) all: 0.317 / Rrim(I) all: 0.61 / Χ2: 0.94 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→30.19 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 23.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 3308 4.84 %RANDOM
Rwork0.1798 ---
obs0.1817 68311 97.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→30.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7135 0 176 235 7546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087444
X-RAY DIFFRACTIONf_angle_d0.89610171
X-RAY DIFFRACTIONf_dihedral_angle_d9.8791153
X-RAY DIFFRACTIONf_chiral_restr0.061245
X-RAY DIFFRACTIONf_plane_restr0.0071293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.920.29541410.27052757X-RAY DIFFRACTION96
1.92-1.950.32231330.27492633X-RAY DIFFRACTION96
1.95-1.980.30731220.24412771X-RAY DIFFRACTION97
1.98-2.010.29531370.23942642X-RAY DIFFRACTION97
2.01-2.040.2741310.22892697X-RAY DIFFRACTION97
2.04-2.080.28231440.21322746X-RAY DIFFRACTION97
2.08-2.120.24861460.20692674X-RAY DIFFRACTION97
2.12-2.160.20921520.19992650X-RAY DIFFRACTION97
2.16-2.210.22641560.19412732X-RAY DIFFRACTION97
2.21-2.260.23881190.1892723X-RAY DIFFRACTION97
2.26-2.320.2291410.18322697X-RAY DIFFRACTION97
2.32-2.380.22741280.18742745X-RAY DIFFRACTION97
2.38-2.450.27551390.18612787X-RAY DIFFRACTION98
2.45-2.530.211320.18322678X-RAY DIFFRACTION98
2.53-2.620.23111450.18722720X-RAY DIFFRACTION98
2.62-2.730.25321340.22732X-RAY DIFFRACTION98
2.73-2.850.27751380.20672702X-RAY DIFFRACTION98
2.85-30.25051360.20672739X-RAY DIFFRACTION98
3-3.190.23521550.20272746X-RAY DIFFRACTION98
3.19-3.430.23671260.19582758X-RAY DIFFRACTION98
3.43-3.780.21611460.16212691X-RAY DIFFRACTION97
3.78-4.320.17881440.14912671X-RAY DIFFRACTION97
4.32-5.440.15521600.14062658X-RAY DIFFRACTION96
5.44-30.190.19371030.14882654X-RAY DIFFRACTION94
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)
10.88840.76140.23811.1710.29381.7313-0.09510.19960.1202-0.19380.12980.12540.2339-0.0955-0.00350.1911-0.0076-0.0430.26050.01260.1753-1.79630.74020.8053
21.17930.67730.571.42590.7641.62550.1693-0.255-0.02530.5328-0.31660.08090.6037-0.3599-0.08320.3659-0.0970.10320.277-0.01650.1988-5.42961.370131.7852
31.11281.05650.04791.26510.69921.61360.1342-0.19840.43380.1113-0.14520.2404-0.19660.0299-0.06520.23660.03780.00870.1629-0.06840.32539.352228.120333.2551
41.08430.62750.09011.12180.83171.391-0.2010.35170.2576-0.33290.2077-0.0451-0.3960.3520.00890.2667-0.0831-0.00480.32920.14140.257617.764923.86891.7967
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 30 through 269)
2X-RAY DIFFRACTION2(chain 'B' and resid 31 through 267)
3X-RAY DIFFRACTION3(chain 'C' and resid 24 through 267)
4X-RAY DIFFRACTION4(chain 'D' and resid 25 through 268)

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