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- PDB-1rks: E. COLI RIBOKINASE IN COMPLEX WITH D-RIBOSE -

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Basic information

Entry
Database: PDB / ID: 1rks
TitleE. COLI RIBOKINASE IN COMPLEX WITH D-RIBOSE
ComponentsPROTEIN (RIBOKINASE)
KeywordsTRANSFERASE / CARBOHYDRATE KINASE / RIBOSE / INDUCED FIT
Function / homology
Function and homology information


ribokinase / ribokinase activity / D-ribose catabolic process / 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
PHOSPHATE ION / alpha-D-ribofuranose / Ribokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.4 Å
AuthorsSigrell, J.A. / Cameron, A.D. / Mowbray, S.L.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Induced fit on sugar binding activates ribokinase.
Authors: Sigrell, J.A. / Cameron, A.D. / Mowbray, S.L.
#1: Journal: Structure / Year: 1998
Title: Structure of Escherichia Coli Ribokinase in Complex with Ribose and Nucleotide 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.
#2: 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.
#3: 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
DepositionMay 17, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
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 / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_special_symmetry / 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 / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (RIBOKINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6604
Polymers32,3201
Non-polymers3403
Water1,60389
1
A: PROTEIN (RIBOKINASE)
hetero molecules

A: PROTEIN (RIBOKINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3218
Polymers64,6412
Non-polymers6806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+2/31
Buried area3660 Å2
ΔGint-33 kcal/mol
Surface area23600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.210, 95.210, 154.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Cell settinghexagonal
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-313-

PO4

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Components

#1: Protein PROTEIN (RIBOKINASE) / E.C.2.7.1.15


Mass: 32320.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Description: THE RBSK GENE WAS CLONED BEHIND AURCE 11 TRP-PROMOTER, FORMING THE PLASMID PJGK10
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 / 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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE SUGAR IS IN THE ALPHA-FURANOSE FORM AND HAS THE UNCOMMON O4'-ENDO PUCKERING.

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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: 48.7 % / Description: RIGIDBODY REFINEMENT FROM 1RKD
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.4
Details: 5 MM RIBOSE, 10 MM MGCL2 IN THE DROP, 0.1 M TRIS-HCL BUFFER, PH 8.4 WITH 2.1-2.4 M NH4H2PO4 AS PRECIPITANT, VAPOR DIFFUSION, HANGING DROP CRYO-SOLUTION: MOTHER LIQUOR CONTAINING 20% GLYCEROL. ...Details: 5 MM RIBOSE, 10 MM MGCL2 IN THE DROP, 0.1 M TRIS-HCL BUFFER, PH 8.4 WITH 2.1-2.4 M NH4H2PO4 AS PRECIPITANT, VAPOR DIFFUSION, HANGING DROP CRYO-SOLUTION: MOTHER LIQUOR CONTAINING 20% GLYCEROL. SOAK-TIME: 2-3 MINUTES.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mMribose1reservoir
210 mMADP1reservoir
30.05 mM1reservoirAlF3
415 mM1reservoirNaF
50.1 Msodium acetate1reservoir
60.25 M1reservoirMgCl2
720 %(v/v)MPD1reservoir
88.8-15 %(w/v)PEG40001reservoir
93-3.5 mg/mlribokinase1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 15, 1997 / Details: MSC MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→29 Å / Num. obs: 16814 / % possible obs: 99.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 30.2
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 5.8 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 134333
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.4→15 Å / SU B: 7.72 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.37 / ESU R Free: 0.28 / Details: BULK SOLVENT CORRECTION APPLIED
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1668 11.1 %RANDOM
Rwork0.229 ---
obs0.231 16740 99.9 %-
Displacement parametersBiso mean: 45.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2236 0 20 89 2345
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.7531
X-RAY DIFFRACTIONp_mcangle_it1.3422
X-RAY DIFFRACTIONp_scbond_it2.8763
X-RAY DIFFRACTIONp_scangle_it3.9825
X-RAY DIFFRACTIONp_plane_restr0.0210.03
X-RAY DIFFRACTIONp_chiral_restr0.1130.15
X-RAY DIFFRACTIONp_singtor_nbd0.1880.3
X-RAY DIFFRACTIONp_multtor_nbd0.260.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1670.3
X-RAY DIFFRACTIONp_planar_tor3.97
X-RAY DIFFRACTIONp_staggered_tor1415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor31.220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / σ(F): 0 / % reflection Rfree: 11.1 % / Rfactor all: 0.231 / Rfactor obs: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 45.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_plane_restr0.03
X-RAY DIFFRACTIONp_chiral_restr0.15
X-RAY DIFFRACTIONp_mcbond_it1
X-RAY DIFFRACTIONp_scbond_it3
X-RAY DIFFRACTIONp_mcangle_it2
X-RAY DIFFRACTIONp_scangle_it5

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