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- PDB-3k3w: Thermostable Penicillin G acylase from Alcaligenes faecalis in or... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3k3w | ||||||
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Title | Thermostable Penicillin G acylase from Alcaligenes faecalis in orthorhombic form | ||||||
![]() | (Penicillin G acylase) x 2 | ||||||
![]() | HYDROLASE / penicillin G acylase | ||||||
Function / homology | ![]() penicillin amidase / penicillin amidase activity / antibiotic biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Varshney, N.K. / Kumar, R.S. / Ignatova, Z. / Dodson, E. / Suresh, C.G. | ||||||
![]() | ![]() Title: Crystallization and X-ray structure analysis of a thermostable penicillin G acylase from Alcaligenes faecalis. Authors: Varshney, N.K. / Kumar, R.S. / Ignatova, Z. / Prabhune, A. / Pundle, A. / Dodson, E. / Suresh, C.G. #1: Journal: Eur.J.Biochem. / Year: 2003 Title: Fragments of pro-peptide activate mature penicillin amidase of Alcaligenes faecalis Authors: Kasche, V. / Galunsky, B. / Ignatova, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.5 KB | Display | ![]() |
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PDB format | ![]() | 123.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.2 KB | Display | ![]() |
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Full document | ![]() | 465.1 KB | Display | |
Data in XML | ![]() | 30.1 KB | Display | |
Data in CIF | ![]() | 39.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ml0C ![]() 1gk9S S: Starting model for refinement 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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Unit cell |
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Components
#1: Protein | Mass: 22329.963 Da / Num. of mol.: 1 / Fragment: UNP residues 27-222 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 62791.953 Da / Num. of mol.: 1 / Fragment: UNP residues 266-816 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.68 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15% PEG8000, 0.1M Tris-Hcl, pH7.5, 60uL of b-octyl- glucopyranoside (0.50% w/v), VAPOR DIFFUSION, HANGING DROP, temperature 303K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 1, 2007 / Details: Mirrors |
Radiation | Monochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.514 Å / Relative weight: 1 |
Reflection | Resolution: 3.306→46.823 Å / Num. all: 12626 / Num. obs: 12602 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Redundancy: 5.73 % / Biso Wilson estimate: 33.34 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 9.23 |
Reflection shell | Resolution: 3.31→3.39 Å / Redundancy: 5.07 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 4.81 / Num. unique all: 806 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GK9 Resolution: 3.31→46.82 Å / Cor.coef. Fo:Fc: 0.822 / Cor.coef. Fo:Fc free: 0.779 / Occupancy max: 1 / Occupancy min: 0 / SU B: 41.193 / SU ML: 0.69 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.747 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.99 Å2 / Biso mean: 40.97 Å2 / Biso min: 15.2 Å2
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Refinement step | Cycle: LAST / Resolution: 3.31→46.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.31→3.39 Å / Total num. of bins used: 20
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