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Yorodumi- PDB-1a5n: K217A VARIANT OF KLEBSIELLA AEROGENES UREASE, CHEMICALLY RESCUED ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a5n | ||||||
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Title | K217A VARIANT OF KLEBSIELLA AEROGENES UREASE, CHEMICALLY RESCUED BY FORMATE AND NICKEL | ||||||
Components |
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Keywords | HYDROLASE / HYDROLASE (UREA AMIDO) / MUTANT / 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 / DIFFERENCE FOURIER / Resolution: 2.4 Å | ||||||
Authors | Pearson, M.A. / Schaller, R.A. / Michel, L.O. / Karplus, P.A. / Hausinger, R.P. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Chemical rescue of Klebsiella aerogenes urease variants lacking the carbamylated-lysine nickel ligand. Authors: Pearson, M.A. / Schaller, R.A. / Michel, L.O. / Karplus, P.A. / Hausinger, R.P. #1: Journal: Acc.Chem.Res. / Year: 1997 Title: 70 Years of Crystalline Urease: What Have We Learned? Authors: Karplus, P.A. / Pearson, M.A. / Hausinger, R.P. #2: Journal: Science / Year: 1995 Title: The Crystal Structure of Urease from Klebsiella Aerogenes Authors: Jabri, E. / Carr, M.B. / Hausinger, R.P. / Karplus, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a5n.cif.gz | 157.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a5n.ent.gz | 121.9 KB | Display | PDB format |
PDBx/mmJSON format | 1a5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/1a5n ftp://data.pdbj.org/pub/pdb/validation_reports/a5/1a5n | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 11100.928 Da / Num. of mol.: 1 / Mutation: K217A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: UREA, UREB, UREC / Plasmid: PKAU17 / Gene (production host): UREA, UREB, UREC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: P18316, 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) / Gene: UREA, UREB, UREC / Plasmid: PKAU17 / Gene (production host): UREA, UREB, UREC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: P18315, urease |
#3: Protein | Mass: 60177.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: UREA, UREB, UREC / Plasmid: PKAU17 / Gene (production host): UREA, UREB, UREC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: P18314, urease |
-Non-polymers , 3 types, 178 molecules
#4: Chemical | #5: Chemical | ChemComp-FMT / | #6: 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: 2.52 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.2 Details: PROTEIN WAS CRYSTALLIZED FROM 100 MM HEPES, PH 7.5, 1.6 M LI2SO4; THEN CRYSTAL WAS SOAKED IN 100 MM HEPES, 500MM FORMATE, PH 7.2, 2.0 M LI2SO4, 1.5 MM NICL2 PH range: 7.2-7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Apr 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.4 Å / Num. obs: 31434 / % possible obs: 100 % / Redundancy: 4 % / Rsym value: 0.099 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.333 / % possible all: 100 |
Reflection | *PLUS Rmerge(I) obs: 0.099 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.333 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 2.4→10 Å / σ(F): 0 Details: ALL NON-BONDED INTERACTIONS INVOLVING THE NICKEL IONS OR FORMATE ION WERE REMOVED DURING REFINEMENT. THE OCCUPANCIES FOR THE NICKEL IONS WERE REFINED WITH A FIXED B-FACTOR OF 17 (ANGSTROMS)**2.
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Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.51 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.226 |