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- PDB-1krc: CRYSTAL STRUCTURE OF KLEBSIELLA AEROGENES UREASE, ITS APOENZYME A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1krc | ||||||
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Title | CRYSTAL STRUCTURE OF KLEBSIELLA AEROGENES UREASE, ITS APOENZYME AND TWO ACTIVE SITE MUTANTS | ||||||
![]() | (UREASE) x 3 | ||||||
![]() | HYDROLASE (UREA AMIDO) / ACTIVE SITE MUTANT / NICKEL METALLOENZYME | ||||||
Function / homology | ![]() urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Jabri, E. / Karplus, P.A. | ||||||
![]() | ![]() Title: Structures of the Klebsiella aerogenes urease apoenzyme and two active-site mutants. Authors: Jabri, E. / Karplus, P.A. #1: ![]() Title: The Crystal Structure of Urease from Klebsiella Aerogenes Authors: Jabri, E. / Carr, M.B. / Hausinger, R.P. / Karplus, P.A. #2: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.7 KB | Display | ![]() |
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PDB format | ![]() | 122.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.8 KB | Display | ![]() |
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Full document | ![]() | 444.5 KB | Display | |
Data in XML | ![]() | 28.4 KB | Display | |
Data in CIF | ![]() | 40.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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. |
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Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 11100.928 Da / Num. of mol.: 1 / Mutation: H(C 320)A / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 11712.239 Da / Num. of mol.: 1 / Mutation: H(C 320)A / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 60299.289 Da / Num. of mol.: 1 / Mutation: H(C 320)A / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 3 types, 162 molecules ![](data/chem/img/NI.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-CO2 / | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | HOH 1, THE CATALYTIC WATER, BRIDGES THE TWO NICKEL IONS. LYS 217 IS COVALENTLY MODIFIED AT NZ BY ...HOH 1, THE CATALYTIC WATER, BRIDGES THE TWO NICKEL IONS. LYS 217 IS COVALENTLY |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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 ℃ / Method: vapor diffusion, hanging drop / pH: 7 / 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: 2.3→99.9 Å / Num. obs: 28672 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.094 |
Reflection | *PLUS Highest resolution: 2.5 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.094 |
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Processing
Software |
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Refinement | Resolution: 2.5→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: 12.2 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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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.18 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.9 |