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Yorodumi- PDB-1ejv: CRYSTAL STRUCTURE OF THE H320Q VARIANT OF KLEBSIELLA AEROGENES UREASE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ejv | ||||||
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Title | CRYSTAL STRUCTURE OF THE H320Q 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: 2.4 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 | 1ejv.cif.gz | 159.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ejv.ent.gz | 128.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ejv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ejv_validation.pdf.gz | 430.5 KB | Display | wwPDB validaton report |
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Full document | 1ejv_full_validation.pdf.gz | 435.2 KB | Display | |
Data in XML | 1ejv_validation.xml.gz | 31.4 KB | Display | |
Data in CIF | 1ejv_validation.cif.gz | 45.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/1ejv ftp://data.pdbj.org/pub/pdb/validation_reports/ej/1ejv | 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: 60399.336 Da / Num. of mol.: 1 / Mutation: H320Q 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: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.02 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: lithium sulfate, Hepes, EDTA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: ADSC / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→100 Å / Num. obs: 31070 / % possible obs: 99 % / Redundancy: 2.7 % |
Reflection shell | Highest resolution: 2.4 Å / Redundancy: 1.6 % / % possible all: 98 |
Reflection | *PLUS Rmerge(I) obs: 0.14 |
Reflection shell | *PLUS % possible obs: 98 % / Rmerge(I) obs: 0.42 |
-Processing
Software |
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Refinement | Resolution: 2.4→10 Å / Rfactor Rwork: 0.181 / Rfactor all: 0.181 / σ(F): 0 | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 10 Å / σ(F): 0 / Rfactor obs: 0.181 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |