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Yorodumi- PDB-4rt5: The crystal structure of a glyoxalase/bleomycin resistance protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rt5 | ||||||
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Title | The crystal structure of a glyoxalase/bleomycin resistance protein/dioxygenase protein from planctomyces limnophilus dsm 3776 | ||||||
Components | Glyoxalase/bleomycin resistance protein/dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / A/B FOLD / CYTOSOLIC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Planctomyces limnophilus DSM 3776 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Wu, R. / Bearden, J. / Kim, Y. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: The crystal structure of a glyoxalase/bleomycin resistance protein/dioxygenase protein from Planctomyces limnophilus dsm 3776 Authors: Wu, R. / Bearden, J. / Kim, Y. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rt5.cif.gz | 96.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rt5.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 4rt5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/4rt5 ftp://data.pdbj.org/pub/pdb/validation_reports/rt/4rt5 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12727.806 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Planctomyces limnophilus DSM 3776 (bacteria) Gene: Plim_1428 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: D5SVJ2, lactoylglutathione lyase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 1.98 Å3/Da / Density % sol: 38.03 % |
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Crystal grow | Temperature: 298 K / pH: 8.5 Details: 0.2 M Magnesium Chloride, 0.1 M TRIS:HCl, pH 8.5, 30% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI 111, CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 30528 / % possible obs: 96.6 % / Redundancy: 4.8 % / Rsym value: 0.036 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.624 / % possible all: 90.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→37.79 Å / σ(F): 1.35 / Phase error: 19.48 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→37.79 Å
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Refine LS restraints |
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LS refinement shell |
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