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Open data
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Basic information
Entry | Database: PDB / ID: 1fwf | ||||||
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Title | KLEBSIELLA AEROGENES UREASE, C319D VARIANT | ||||||
![]() | (UREASE) x 3 | ||||||
![]() | HYDROLASE / HYDROLASE(UREA AMIDO) / MUTANT / NICKEL METALLOENZYME | ||||||
Function / homology | ![]() urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Pearson, M.A. / Karplus, P.A. | ||||||
![]() | ![]() Title: Structures of Cys319 variants and acetohydroxamate-inhibited Klebsiella aerogenes urease. Authors: Pearson, M.A. / Michel, L.O. / Hausinger, R.P. / Karplus, P.A. #1: ![]() Title: Structures of the Klebsiella Aerogenes Urease Apoenzyme and Two Active-Site Mutants Authors: Jabri, E. / Karplus, P.A. #2: ![]() Title: The Crystal Structure of Urease from Klebsiella Aerogenes Authors: Jabri, E. / Carr, M.B. / Hausinger, R.P. / Karplus, P.A. #3: ![]() Title: Site-Directed Mutagenesis of the Active Site Cysteine in Klebsiella Aerogenes Urease Authors: Martin, P.R. / Hausinger, R.P. #4: ![]() Title: Identification of the Essential Cysteine Residue in Klebsiella Aerogenes Urease Authors: Todd, M.J. / Hausinger, R.P. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160 KB | Display | ![]() |
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PDB format | ![]() | 124.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.1 KB | Display | ![]() |
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Full document | ![]() | 439.2 KB | Display | |
Data in XML | ![]() | 29 KB | Display | |
Data in CIF | ![]() | 42.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1fwaC ![]() 1fwbC ![]() 1fwcC ![]() 1fwdC ![]() 1fweC ![]() 1fwgC ![]() 1fwhC ![]() 1fwjC C: citing same article ( |
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Similar 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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Components
#1: Protein | Mass: 11100.928 Da / Num. of mol.: 1 / Mutation: C(C 319)D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 11712.239 Da / Num. of mol.: 1 / Mutation: C(C 319)D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
#3: Protein | Mass: 60421.297 Da / Num. of mol.: 1 / Mutation: C(C 319)D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Compound details | THIS MODEL IS THAT OF THE C319D MUTANT AT 2.0 ANGSTROMS. THREE NONIDENTICAL CHAINS, GAMMA (A), BETA ...THIS MODEL IS THAT OF THE C319D MUTANT AT 2.0 ANGSTROMS. THREE NONIDENTIC | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 |
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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 | Num. obs: 52745 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 92 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.292 |
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Processing
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Refinement | Resolution: 2→10 Å / σ(F): 0 Details: ALL NON-BONDED INTERACTIONS WERE REMOVED BETWEEN THE ACTIVE SITE NICKEL IONS AND NICKEL-BOUND WATERS 500, 501, 502. THE OCCUPANCIES FOR ACTIVE SITE WATERS HOH 500 - HOH 502 WERE REFINED WITH ...Details: ALL NON-BONDED INTERACTIONS WERE REMOVED BETWEEN THE ACTIVE SITE NICKEL IONS AND NICKEL-BOUND WATERS 500, 501, 502. THE OCCUPANCIES FOR ACTIVE SITE WATERS HOH 500 - HOH 502 WERE REFINED WITH A FIXED B-FACTOR OF 20 ANGSTROMS**2. THE REFINED OCCUPANCIES FOR THESE WATERS SUGGEST NEARLY FULL OCCUPANCY FOR EACH OF THEM, ALTHOUGH THEY ARE POSITIONED TOO CLOSE (~ 2.0 ANGSTROMS APART) FOR SIMULTANEOUS OCCUPANCY. THE OCCUPANCIES FOR ACTIVE SITE WATERS HOH 500 - HOH 502 WERE REFINED WITH A FIXED B-FACTOR OF 20 ANGSTROMS**2. THE REFINED OCCUPANCIES FOR THESE WATERS SUGGEST NEARLY FULL OCCUPANCY FOR EACH OF THEM, ALTHOUGH THEY ARE POSITIONED TOO CLOSE (~ 2.0 ANGSTROMS APART) FOR SIMULTANEOUS OCCUPANCY.
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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