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- PDB-1rka: THE APO FORM OF E. COLI RIBOKINASE -

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Basic information

Entry
Database: PDB / ID: 1rka
TitleTHE APO FORM OF E. COLI RIBOKINASE
ComponentsPROTEIN (RIBOKINASE)
KeywordsTRANSFERASE / CARBOHYDRATE KINASE / RIBOSE / NUCLEOTIDE BINDING / INDUCED FIT
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 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.
#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
DepositionMar 22, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 13, 2019Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.5Aug 23, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (RIBOKINASE)


Theoretical massNumber of molelcules
Total (without water)32,3201
Polymers32,3201
Non-polymers00
Water2,216123
1
A: PROTEIN (RIBOKINASE)

A: PROTEIN (RIBOKINASE)


Theoretical massNumber of molelcules
Total (without water)64,6412
Polymers64,6412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2170 Å2
ΔGint-19 kcal/mol
Surface area24340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.970, 61.970, 127.834
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121

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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) / Strain: MRI240
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.1 Å3/Da / Density % sol: 40.2 %
Crystal growpH: 4.8
Details: CRYSTALS WERE GROWN IN 22-33% PEG 2000, MONO-METHYLETHER AS PRECIPITANT AND BUFFERED TO PH 4.8 WITH 0.1 M NA ACETATE. CRYO-PROTECTANT: MOTHER LIQUID ALSO CONTAINING 15% ETHYLENEGLYCOL. SOAK-TIME: 2-3 MINUTES.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
111 mg/mlribokinase1drop
220 mMTris-HCl1drop
30.2 M1dropNaCl
40.1 MNa acetate1reservoir
50.2 MNH4 acetate1reservoir
622-33 %mPEG20001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.996
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1998 / Details: MIRRORS
RadiationMonochromator: SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.996 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. obs: 12644 / % possible obs: 96.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.6
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 6.7 / % possible all: 87.5
Reflection
*PLUS
Num. measured all: 62741
Reflection shell
*PLUS
% possible obs: 87.5 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.3refinement
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: 2.3→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.253 619 4.7 %RANDOM
Rwork0.21 ---
all-12644 --
obs-12644 96.3 %-
Solvent computationSolvent model: EXPONENTIAL SCALING / Bsol: 45.9 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1--2.84 Å2-1.66 Å20 Å2
2---2.84 Å20 Å2
3---5.685 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2236 0 0 123 2359
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.76
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.11.5
X-RAY DIFFRACTIONx_mcangle_it1.72
X-RAY DIFFRACTIONx_scbond_it1.82
X-RAY DIFFRACTIONx_scangle_it2.52.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.45
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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