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- PDB-1rkd: E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP -

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Basic information

Entry
Database: PDB / ID: 1rkd
TitleE. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP
ComponentsRIBOKINASE
KeywordsCARBOHYDRATE KINASE / RIBOSE / NUCLEOTIDE BINDING / TRANSFERASE
Function / homology
Function and homology information


ribokinase / ribokinase activity / D-ribose catabolic process / protein homodimerization activity / ATP binding / metal ion binding / 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 / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / alpha-D-ribofuranose / Ribokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.84 Å
AuthorsSigrell, J.A. / Cameron, A.D. / Jones, T.A. / Mowbray, S.L.
Citation
Journal: Structure / Year: 1998
Title: Structure of Escherichia coli ribokinase in complex with ribose and dinucleotide determined to 1.8 A resolution: insights into a new family of kinase structures.
Authors: Sigrell, J.A. / Cameron, A.D. / Jones, T.A. / Mowbray, S.L.
#1: Journal: Protein Sci. / Year: 1997
Title: Purification, Characterization, and Crystallization of Escherichia Coli Ribokinase
Authors: Sigrell, J.A. / Cameron, A.D. / Jones, T.A. / Mowbray, S.L.
#2: Journal: J.Biol.Chem. / Year: 1986
Title: Ribokinase from Escherichia Coli K12. Nucleotide Sequence and Overexpression of the Rbsk Gene and Purification of Ribokinase
Authors: Hope, J.N. / Bell, A.W. / Hermodson, M.A. / Groarke, J.M.
History
DepositionNov 29, 1997Processing site: BNL
Revision 1.0Mar 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0885
Polymers32,3201
Non-polymers7674
Water3,261181
1
A: RIBOKINASE
hetero molecules

A: RIBOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,17510
Polymers64,6412
Non-polymers1,5358
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+2/31
Buried area5260 Å2
ΔGint-47 kcal/mol
Surface area23120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.400, 95.400, 154.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-313-

PO4

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Components

#1: Protein RIBOKINASE


Mass: 32320.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12
Description: THE RBSK GENE WAS CLONED BEHIND A TRP-PROMOTER, FORMING THE PLASMID PJGK10
Cell line: S2 / Cellular location: CYTOPLASM / Gene: RBSK / Plasmid: PJGK10 / Production host: Escherichia coli (E. coli) / Strain (production host): MRI240 / References: UniProt: P0A9J6, 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
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
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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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: 3.1 Å3/Da / Density % sol: 49 %
Crystal growpH: 8.4
Details: CRYSTALS WERE GROWN IN THE PRESENCE OF 0.5 MM RIBOSE, 10 MM AMP-PNP AND 10 MM MGCL2 USING 2.1-2.4 M NH4H2PO4 AS PRECIPITANT AND BUFFERED TO PH 8.4 WITH 0.1 M TRIS-HCL.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Sigrell, J.A., (1997) Protein Sci., 6, 2474.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15.5 mg/mlribokinase1drop
210 mMTris-HCl1drop
30.1 M1dropNaCl
40.5 mMribose1drop
510 mMLi AMP-PNP1drop
610 mM1dropMgCl2
71.05-1.2 M1dropNH4H2PO4
80.05 MTris-HCl1drop
9ammonium phosphate1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8893
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8893 Å / Relative weight: 1
ReflectionResolution: 1.84→30 Å / Num. obs: 35015 / % possible obs: 95.5 % / Redundancy: 7.5 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 30.2
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 7.4 / % possible all: 97.8
Reflection
*PLUS
Num. measured all: 279852
Reflection shell
*PLUS
% possible obs: 97.8 %

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.84→28 Å / Cross valid method: THROUGHOUT
Details: THE BULK SOLVENT CORRECTION WAS CALCULATED IN X-PLOR. AMP-PNP WAS INCLUDED IN THE CRYSTALLIZATION MIXTURE, BUT THE GAMMA-PHOSPHATE COULD NOT BE DETECTED. THE AUTHORS THEREFORE TREAT ...Details: THE BULK SOLVENT CORRECTION WAS CALCULATED IN X-PLOR. AMP-PNP WAS INCLUDED IN THE CRYSTALLIZATION MIXTURE, BUT THE GAMMA-PHOSPHATE COULD NOT BE DETECTED. THE AUTHORS THEREFORE TREAT HYDROLYSED ATP-ANALOGUE AS ADP IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3542 10 %RANDOM
Rwork0.22 ---
obs0.221 35013 95.5 %-
Displacement parametersBiso mean: 29 Å2
Refine analyzeLuzzati sigma a obs: 0.07 Å
Refinement stepCycle: LAST / Resolution: 1.84→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 47 181 2476
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0280.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.42
X-RAY DIFFRACTIONp_mcangle_it22.5
X-RAY DIFFRACTIONp_scbond_it3.54
X-RAY DIFFRACTIONp_scangle_it56
X-RAY DIFFRACTIONp_plane_restr0.020.03
X-RAY DIFFRACTIONp_chiral_restr0.130.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.150.3
X-RAY DIFFRACTIONp_planar_tor4.27
X-RAY DIFFRACTIONp_staggered_tor16.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.620
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS

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