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- PDB-1tyy: Crystal structure of aminoimidazole riboside kinase from Salmonel... -

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Basic information

Entry
Database: PDB / ID: 1tyy
TitleCrystal structure of aminoimidazole riboside kinase from Salmonella enterica
Componentsputative sugar kinase
KeywordsTRANSFERASE / ribokinase fold / alpha/beta
Function / homology
Function and homology information


aminoimidazole riboside kinase / phosphotransferase activity, alcohol group as acceptor / kinase activity / phosphorylation / ATP binding / metal ion binding
Similarity search - Function
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
: / Aminoimidazole riboside kinase
Similarity search - Component
Biological speciesSalmonella typhimurium LT2 (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsZhang, Y. / Dougherty, M. / Downs, D.M. / Ealick, S.E.
CitationJournal: STRUCTURE / Year: 2004
Title: Crystal Structure of an Aminoimidazole Riboside Kinase from Salmonella enterica; Implications for the Evolution of the Ribokinase Superfamily
Authors: Zhang, Y. / Dougherty, M. / Downs, D.M. / Ealick, S.E.
History
DepositionJul 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative sugar kinase
B: putative sugar kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4106
Polymers73,2532
Non-polymers1564
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-7 kcal/mol
Surface area23500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.430, 53.987, 89.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein putative sugar kinase


Mass: 36626.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium LT2 (unknown)
Species: Salmonella typhimuriumSalmonella enterica subsp. enterica
Strain: CT18 / Gene: stm4066 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: Q8ZKR2, fructokinase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: PEG3350, potassium sulfate, tertiary-butanol or isopropanol, DTT, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 18143 / Num. obs: 18143 / % possible obs: 85.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 43.9 Å2 / Rsym value: 0.069 / Net I/σ(I): 20.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 1479 / Rsym value: 0.289 / % possible all: 69.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→32.01 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 516965 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1740 10 %RANDOM
Rwork0.222 ---
all0.229 17549 --
obs0.222 17549 82.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.9817 Å2 / ksol: 0.285586 e/Å3
Displacement parametersBiso mean: 71.9 Å2
Baniso -1Baniso -2Baniso -3
1-23.19 Å20 Å20 Å2
2--7.64 Å20 Å2
3----30.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.6→32.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4371 0 4 54 4429
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
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 NCSNCS model details: CONSTR
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.477 233 10.3 %
Rwork0.41 2036 -
obs--56.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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