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Yorodumi- PDB-1ejr: CRYSTAL STRUCTURE OF THE D221A VARIANT OF KLEBSIELLA AEROGENES UREASE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ejr | ||||||
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Title | CRYSTAL STRUCTURE OF THE D221A VARIANT OF KLEBSIELLA AEROGENES UREASE | ||||||
Components |
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Keywords | HYDROLASE / alpha-beta barrel / nickel metalloenzyme | ||||||
Function / homology | Function and homology information urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm Similarity search - Function | ||||||
Biological species | Klebsiella aerogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Pearson, M.A. / Park, I.S. / Schaller, R.A. / Michel, L.O. / Karplus, P.A. / Hausinger, R.P. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Kinetic and structural characterization of urease active site variants. Authors: Pearson, M.A. / Park, I.S. / Schaller, R.A. / Michel, L.O. / Karplus, P.A. / Hausinger, R.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ejr.cif.gz | 160.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ejr.ent.gz | 129 KB | Display | PDB format |
PDBx/mmJSON format | 1ejr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ejr_validation.pdf.gz | 433.2 KB | Display | wwPDB validaton report |
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Full document | 1ejr_full_validation.pdf.gz | 438 KB | Display | |
Data in XML | 1ejr_validation.xml.gz | 31.5 KB | Display | |
Data in CIF | 1ejr_validation.cif.gz | 45.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/1ejr ftp://data.pdbj.org/pub/pdb/validation_reports/ej/1ejr | HTTPS FTP |
-Related 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: 60365.344 Da / Num. of mol.: 1 / Mutation: D221A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P18314, urease | ||
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#2: Protein | Mass: 11125.690 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P18315, urease | ||
#3: Protein | Mass: 11100.928 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P18316, urease | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal |
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Crystal grow |
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Crystal grow | *PLUS Temperature: 25 ℃ / pH: 7 / Details: Jabri, E., (1992) J.Mol.Biol., 227, 934. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||
Reflection | Resolution: 2→100 Å / Num. obs: 55503 / % possible obs: 100 % / Redundancy: 10.8 % | |||||||||
Reflection shell | Highest resolution: 2 Å / Redundancy: 10.6 % / % possible all: 100 | |||||||||
Reflection | *PLUS Rmerge(I) obs: 0.09 | |||||||||
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.58 |
-Processing
Software | Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||
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Refinement | Resolution: 2→10 Å / Rfactor Rwork: 0.161 / Rfactor all: 0.161 / σ(F): 0 | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 10 Å / σ(F): 0 / Rfactor obs: 0.161 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |