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Yorodumi- PDB-1tz3: crystal structure of aminoimidazole riboside kinase complexed wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tz3 | ||||||
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Title | crystal structure of aminoimidazole riboside kinase complexed with aminoimidazole riboside | ||||||
Components | putative sugar kinase | ||||||
Keywords | TRANSFERASE / ribokinase fold / alpha/beta | ||||||
Function / homology | Function and homology information aminoimidazole riboside kinase / fructokinase activity / fructose metabolic process / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Salmonella typhimurium LT2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Zhang, Y. / Dougherty, M. / Downs, D.M. / Ealick, S.E. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tz3.cif.gz | 118.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tz3.ent.gz | 91 KB | Display | PDB format |
PDBx/mmJSON format | 1tz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tz3_validation.pdf.gz | 466.2 KB | Display | wwPDB validaton report |
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Full document | 1tz3_full_validation.pdf.gz | 490 KB | Display | |
Data in XML | 1tz3_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 1tz3_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/1tz3 ftp://data.pdbj.org/pub/pdb/validation_reports/tz/1tz3 | HTTPS FTP |
-Related structure data
Related structure data | 1tyySC 1tz6C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36626.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium LT2 (bacteria) / Species: Salmonella typhimurium / 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 / #3: Chemical | ChemComp-AIS / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 14276 / Num. obs: 14276 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 141.7 Å2 / Rsym value: 0.049 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 1152 / Rsym value: 0.289 / % possible all: 75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TYY Resolution: 2.9→28.77 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 337246.54 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.1899 Å2 / ksol: 0.307995 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→28.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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