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- PDB-1rk2: E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP, SOLVED IN SPACE... -

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Basic information

Entry
Database: PDB / ID: 1rk2
TitleE. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP, SOLVED IN SPACE GROUP P212121
ComponentsRIBOKINASE
KeywordsTRANSFERASE / CARBOHYDRATE KINASE / RIBOSE / INDUCED FIT / DOMAIN RE-ARRANGEMENTS
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 / TETRAFLUOROALUMINATE ION / alpha-D-ribofuranose / Ribokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 20, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 1, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
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
B: RIBOKINASE
C: RIBOKINASE
D: RIBOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,10020
Polymers129,2824
Non-polymers2,81816
Water7,368409
1
A: RIBOKINASE
B: RIBOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,05010
Polymers64,6412
Non-polymers1,4098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-46 kcal/mol
Surface area23690 Å2
MethodPISA
2
C: RIBOKINASE
D: RIBOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,05010
Polymers64,6412
Non-polymers1,4098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-44 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.201, 62.492, 337.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.751594, -0.659461, 0.014751), (-0.659626, 0.751432, -0.01561), (-0.00079, -0.021463, -0.999769)23.99, 10.973, 188.90601
2given(-0.719392, 0.693908, -0.031096), (0.692426, 0.719959, 0.046954), (0.05497, 0.012247, -0.998413)12.921, -8.801, 273.461
3given(-0.071828, 0.997288, 0.01604), (-0.996018, -0.070866, -0.054094), (-0.052811, -0.019861, 0.998407)22.934, -7.285, -84.357

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
RIBOKINASE /


Mass: 32320.393 Da / Num. of mol.: 4
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 / alpha-D-ribose / D-ribose / ribose / Ribose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 4 / Source method: isolated from a natural 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

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Non-polymers , 4 types, 421 molecules

#3: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.2 Å3/Da / Density % sol: 33.2 %
Crystal growpH: 4.8
Details: CRYSTALS WERE GROWN IN THE PRESENCE OF 5 MM RIBOSE, 10 MM ADP, 0.05 MM ALF4 AND 15 MM NAF USING 8.8-15% PEG 4000, 0.25 M MGCL2 AND 20% MPD IN 0.1 M TRIS- HCL BUFFERED TO PH 4.8.
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13-3.5 mg/mlribokinase1drop
25 mMribose1reservoir
310 mMADP1reservoir
40.05 mMAIF31reservoir
515 mM1reservoirNaF
60.1 Msodium acetate1reservoir
70.25 M1reservoirMgCl2
820 %(v/v)MPD1reservoir
98.8-15 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9058
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1998 / Details: BENT MIRROR
RadiationMonochromator: TRIANGULAR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9058 Å / Relative weight: 1
ReflectionResolution: 2.25→13 Å / Num. obs: 55979 / % possible obs: 99.1 % / Redundancy: 4 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 17
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 4 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 3.9 / % possible all: 98.8
Reflection
*PLUS
Num. measured all: 188129
Reflection shell
*PLUS
% possible obs: 98.8 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RKD: RESIDUES 4-9, 44-93, 123-241 AND 254-309

1rkd


Resolution: 2.25→13 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 2972122.44 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: TARGET WAS MLF USING AMPLITUDES. THE MAIN-CHAIN OF RESIDUES 5-13, 43-93, 116- 198, 205-235, 240-243, 247-305 AND ALF 315 WERE RESTRAINED WITH A WEIGHT OF 100.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2815 5 %RANDOM
Rwork0.228 ---
obs-55979 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.98 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å20 Å2
2--5.01 Å20 Å2
3----6.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.25→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8972 0 172 409 9553
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)Weight Biso Weight position
11RESTRAINTS2.10.062100
223.30.091050
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 512 5.6 %
Rwork0.254 8650 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3COMB_ADP_MG.PARCOMB_ADP_MG.TOP
X-RAY DIFFRACTION4RIB.PARRIB.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Rfactor Rwork: 0.225

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