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- PDB-3mji: Activation of catalytic cysteine without a base in a Mutant Penic... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mji | ||||||
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Title | Activation of catalytic cysteine without a base in a Mutant Penicillin Acylase Precursor | ||||||
![]() | Penicillin acylase | ||||||
![]() | HYDROLASE / ZYMOGEN / PENICILLIN / AUTOPROTEOLYSIS / ANTIBIOTIC RESISTANCE / CATALYSIS / PENICILLIN V ACYLASE / AMIDASE | ||||||
Function / homology | ![]() penicillin amidase / penicillin amidase activity / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pathak, M.C. / Suresh, C.G. / Dodson, G.G. / Murshudov, G.N. | ||||||
![]() | ![]() Title: Activation of catalytic cysteine without a base in a Mutant Penicillin Acylase Precursor Authors: Pathak, M.C. / Suresh, C.G. / Dodson, G.G. / Murshudov, G.N. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Cloning, preparation and preliminary crystallographic studies of Penicillin V Acylase autoproteolytic processing mutants Authors: Chandra, P.M. / Brannigan, J.A. / Prabhune, A. / Pundle, A. / Turkenburg, J.P. / Dodson, G.G. / Suresh, C.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 263.4 KB | Display | ![]() |
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PDB format | ![]() | 214.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464 KB | Display | ![]() |
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Full document | ![]() | 492 KB | Display | |
Data in XML | ![]() | 50.9 KB | Display | |
Data in CIF | ![]() | 71.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mik |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37530.535 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.06 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.4 / Details: pH 6.4, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Detector: CCD | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.5→50 Å / Num. obs: 62997 / % possible obs: 99.9 % / Rsym value: 0.086 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.443 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.557 Å / Total num. of bins used: 20
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