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Yorodumi- PDB-1kra: CRYSTAL STRUCTURE OF KLEBSIELLA AEROGENES UREASE, ITS APOENZYME A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kra | |||||||||
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Title | CRYSTAL STRUCTURE OF KLEBSIELLA AEROGENES UREASE, ITS APOENZYME AND TWO ACTIVE SITE MUTANTS | |||||||||
Components | (UREASE) x 3 | |||||||||
Keywords | HYDROLASE (UREA AMIDO) / APOENZYME / 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: 2.3 Å | |||||||||
Authors | Jabri, E. / Karplus, P.A. | |||||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Structures of the Klebsiella aerogenes urease apoenzyme and two active-site mutants. Authors: Jabri, E. / Karplus, P.A. #1: 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. #2: Journal: J.Mol.Biol. / Year: 1992 Title: Preliminary Crystallographic Studies of Urease from Jack Bean and from Klebsiella Aerogenes Authors: Jabri, E. / Lee, M.H. / 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 | 1kra.cif.gz | 154.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kra.ent.gz | 121.7 KB | Display | PDB format |
PDBx/mmJSON format | 1kra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kra_validation.pdf.gz | 429.7 KB | Display | wwPDB validaton report |
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Full document | 1kra_full_validation.pdf.gz | 436.8 KB | Display | |
Data in XML | 1kra_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 1kra_validation.cif.gz | 40.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/1kra ftp://data.pdbj.org/pub/pdb/validation_reports/kr/1kra | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO C 282 / 2: CIS PROLINE - PRO C 303 / 3: CIS PROLINE - PRO C 470 | ||||||||
Details | THREE NONIDENTICAL CHAINS, GAMMA (A), BETA (B), AND ALPHA (C) FORM ONE (ABC)-UNIT. THE ASYMMETRIC UNIT CONTAINS ONE (ABC)-UNIT. |
-Components
#1: Protein | Mass: 11100.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Klebsiella aerogenes (bacteria) / Organ: BEAN / References: UniProt: P18316, urease |
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#2: Protein | Mass: 11712.239 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Klebsiella aerogenes (bacteria) / Organ: BEAN / References: UniProt: P18315, urease |
#3: Protein | Mass: 60366.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Klebsiella aerogenes (bacteria) / Organ: BEAN / References: UniProt: P18314, urease |
#4: Water | ChemComp-HOH / |
Compound details | 1KAU= 2.2 ANGSTROM STRUCTURE-COMPLETE NICKEL COORDINATI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.7 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 25 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Jabri, E., (1992) J.Mol.Biol., 227, 934. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 Å |
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Detector | Type: XUONG-HAMLIN MULTIWIRE MARK II / Detector: AREA DETECTOR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→99.9 Å / Num. obs: 35214 / % possible obs: 98 % / Observed criterion σ(F): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.155 |
Reflection | *PLUS Highest resolution: 2.3 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.155 |
-Processing
Software |
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Refinement | Resolution: 2.3→10 Å / σ(F): 0 Details: RESIDUES 308 - 330 IN CHAIN C HAVE HIGH B VALUES. THEY CORRESPOND TO A MOBILE LOOP NEAR THE ACTIVE SITE.
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Displacement parameters | Biso mean: 8.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.9 |