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Yorodumi- PDB-1krb: CRYSTAL STRUCTURE OF KLEBSIELLA AEROGENES UREASE, ITS APOENZYME A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1krb | ||||||
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Title | CRYSTAL STRUCTURE OF KLEBSIELLA AEROGENES UREASE, ITS APOENZYME AND TWO ACTIVE SITE MUTANTS | ||||||
Components | (UREASE) x 3 | ||||||
Keywords | HYDROLASE / ACTIVE SITE MUTANT / NICKEL METALLOENZYME / HYDROLASE (UREA AMIDO) | ||||||
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: 2.5 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: Protein Sci. / Year: 1993 Title: Site-Directed Mutagenesis of Klebsiella Aerogenes Urease: Identification of Histidine Residues that Appear to Function in Nickel Ligation, Substrate Binding, and Catalysis Authors: Park, I.-L. / Hausinger, R.P. #3: 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 | 1krb.cif.gz | 151.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1krb.ent.gz | 123.6 KB | Display | PDB format |
PDBx/mmJSON format | 1krb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/1krb ftp://data.pdbj.org/pub/pdb/validation_reports/kr/1krb | 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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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 / Mutation: H(C 219)A / 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 / Mutation: H(C 219)A / Source method: isolated from a natural source / Source: (natural) Klebsiella aerogenes (bacteria) / Organ: BEAN / References: UniProt: P18315, urease | ||||
#3: Protein | Mass: 60342.289 Da / Num. of mol.: 1 / Mutation: H(C 219)A / Source method: isolated from a natural source / Source: (natural) Klebsiella aerogenes (bacteria) / Organ: BEAN / References: UniProt: P18314, urease | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Compound details | RESIDUE KCX C 217 IS A MODIFIED LYSINE WHICH IS CARBAMYLATED AT THE ZETA-AMINO GROUP. THIS MODEL IS ...RESIDUE KCX C 217 IS A MODIFIED LYSINE WHICH IS CARBAMYLAT | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.73 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 / 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: 27404 / % possible obs: 98 % / Observed criterion σ(F): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.095 |
Reflection | *PLUS Highest resolution: 2.5 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.095 |
-Processing
Software |
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Refinement | Resolution: 2.5→10 Å / σ(F): 0
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Displacement parameters | Biso mean: 10.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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