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- PDB-9m8t: Crystal structure of the ribokinase RBK1 in complex with ADP from... -

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Basic information

Entry
Database: PDB / ID: 9m8t
TitleCrystal structure of the ribokinase RBK1 in complex with ADP from Saccharomyces cerevisiae
ComponentsRibokinase
KeywordsPROTEIN BINDING / 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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Ribokinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 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 12, 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)75,06910
Polymers73,9302
Non-polymers1,1398
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-96 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.640, 123.150, 168.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 117 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 8% Tacsimate pH 8.0, 20% PEG 3350, 0.02M Calcium chloride dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.66→40.82 Å / Num. obs: 24435 / % possible obs: 98.7 % / Redundancy: 13 % / CC1/2: 0.99 / Net I/σ(I): 15.2
Reflection shellResolution: 2.66→2.73 Å / Num. unique obs: 1771 / CC1/2: 0.878

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→31.88 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2789 1217 5.01 %
Rwork0.2164 --
obs0.2195 24282 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.66→31.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5089 0 68 109 5266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125247
X-RAY DIFFRACTIONf_angle_d1.2127120
X-RAY DIFFRACTIONf_dihedral_angle_d18.9141914
X-RAY DIFFRACTIONf_chiral_restr0.067814
X-RAY DIFFRACTIONf_plane_restr0.006916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.770.4261390.38012465X-RAY DIFFRACTION96
2.77-2.890.36271150.29462579X-RAY DIFFRACTION99
2.89-3.040.35981330.30342566X-RAY DIFFRACTION99
3.04-3.240.33561420.2672568X-RAY DIFFRACTION100
3.24-3.480.36651430.26192527X-RAY DIFFRACTION98
3.48-3.830.28511270.25922434X-RAY DIFFRACTION93
3.83-4.390.32851330.20282567X-RAY DIFFRACTION98
4.39-5.520.19411560.17132633X-RAY DIFFRACTION100
5.53-31.880.23861290.17252726X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 22.0256 Å / Origin y: 30.7205 Å / Origin z: 82.7041 Å
111213212223313233
T0.4331 Å20.0212 Å20.0193 Å2-0.5246 Å20.032 Å2--0.5093 Å2
L-0.1108 °20.0658 °20.0309 °2-0.7751 °2-0.3915 °2--0.664 °2
S-0.0094 Å °0.0466 Å °0.0506 Å °0.0174 Å °0.0555 Å °0.042 Å °-0.0434 Å °-0.0622 Å °-0 Å °
Refinement TLS groupSelection details: all

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