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- PDB-9u3w: Crystal structure of the ribokinase RBK1 in complex with ribose f... -

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Basic information

Entry
Database: PDB / ID: 9u3w
TitleCrystal structure of the ribokinase RBK1 in complex with ribose from Saccharomyces cerevisiae
ComponentsRibokinase
KeywordsTRANSFERASE / ribokinase
Function / homology
Function and homology information


Pentose phosphate pathway / ribokinase / ribokinase activity / D-ribose catabolic process / ATP binding / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ribokinase / Ribokinase/fructokinase / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like
Similarity search - Domain/homology
alpha-D-ribofuranose / Ribokinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsYang, X.Y. / Liu, X.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Structural and biochemical insights into the molecular mechanism of ribokinase RBK1 from Saccharomyces cerevisiae.
Authors: Zhen, S. / Zhang, Z. / Fan, Y. / Li, Y. / Liu, C. / Guo, F. / Zhu, Y. / Wang, Y. / Zhang, J. / Xie, J. / Zhou, H. / Yang, X. / Liu, X.
History
DepositionMar 18, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 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: Ribokinase
B: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2304
Polymers73,9302
Non-polymers3002
Water00
1
A: Ribokinase
hetero molecules

B: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2304
Polymers73,9302
Non-polymers3002
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_544-x+1/2,y-1/2,-z-1/21
Buried area3220 Å2
ΔGint-19 kcal/mol
Surface area26750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.840, 169.060, 117.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Ribokinase / RK


Mass: 36964.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RBK1, YCR036W, YCR36W, YCR523 / Production host: Escherichia coli (E. coli) / References: UniProt: P25332, ribokinase
#2: Sugar ChemComp-RIB / alpha-D-ribofuranose / alpha-D-ribose / D-ribose / ribose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DRibfaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-ribofuranoseCOMMON NAMEGMML 1.0
a-D-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.2M Sodium formate, 0.1M Bicine pH 8.6, 24% PEG 5000, 0.04% 1,2-Diaminocyclohexane sulfate, 0.04% Diloxanide furoate, 0.04% Fumaric acid, 0.04% Spermine, 0.04% Sulfaguanidine, 0.004M HEPES sodium pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.978797 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978797 Å / Relative weight: 1
ReflectionResolution: 2.91→84.53 Å / Num. obs: 17881 / % possible obs: 99.2 % / Redundancy: 12.3 % / CC1/2: 0.997 / Net I/σ(I): 14.3
Reflection shellResolution: 2.91→2.99 Å / Num. unique obs: 1303 / CC1/2: 0.557

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→36.47 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2935 890 4.98 %
Rwork0.2402 --
obs0.2426 17881 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.91→36.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4649 0 20 0 4669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044761
X-RAY DIFFRACTIONf_angle_d0.8646493
X-RAY DIFFRACTIONf_dihedral_angle_d7.771662
X-RAY DIFFRACTIONf_chiral_restr0.051773
X-RAY DIFFRACTIONf_plane_restr0.009846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-3.090.45531530.39052802X-RAY DIFFRACTION100
3.09-3.330.34311360.3072836X-RAY DIFFRACTION100
3.33-3.670.32781520.28442765X-RAY DIFFRACTION97
3.67-4.20.3271610.2552749X-RAY DIFFRACTION97
4.2-5.280.24051330.21052897X-RAY DIFFRACTION100
5.28-36.470.27531550.21672942X-RAY DIFFRACTION98

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