[English] 日本語
![](img/lk-miru.gif)
- PDB-3ml0: Thermostable Penicillin G acylase from Alcaligenes faecalis in te... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3ml0 | ||||||
---|---|---|---|---|---|---|---|
Title | Thermostable Penicillin G acylase from Alcaligenes faecalis in tetragonal form | ||||||
![]() |
| ||||||
![]() | 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. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 152.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 119.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3k3wC ![]() 1gk9S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 22258.885 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 62791.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-CA / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.74 % |
---|---|
Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15% PEG 8000, 0.1M Tris-Hcl pH7.5, 100uL b-octyl-glucopyranoside (0.50% w/v), vapor diffusion, hanging drop, temperature 303K |
-Data collection
Diffraction | Mean temperature: 295 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 7, 2006 / 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: 3.5→82.2 Å / Num. obs: 14860 / % possible obs: 90.8 % / Observed criterion σ(F): 1 / Redundancy: 2.25 % / Biso Wilson estimate: 29.99 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 7.42 |
Reflection shell | Resolution: 3.499→3.59 Å / Redundancy: 2.01 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 3.08 / Num. unique all: 13376 / % possible all: 89.67 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1GK9 Resolution: 3.5→20 Å / Cor.coef. Fo:Fc: 0.849 / Cor.coef. Fo:Fc free: 0.823 / Occupancy max: 1 / Occupancy min: 0 / SU B: 35.918 / SU ML: 0.547 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.716 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 65.2 Å2 / Biso mean: 47.781 Å2 / Biso min: 20 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→20 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.499→3.59 Å / Total num. of bins used: 20
|