[English] 日本語
![](img/lk-miru.gif)
- PDB-2x3l: Crystal Structure of the Orn_Lys_Arg decarboxylase family protein... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2x3l | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Orn_Lys_Arg decarboxylase family protein SAR0482 from Methicillin-resistant Staphylococcus aureus | ||||||
![]() | ORN/LYS/ARG DECARBOXYLASE FAMILY PROTEIN | ||||||
![]() | LYASE | ||||||
Function / homology | ![]() Aspartate Aminotransferase, domain 1 - #150 / Molybdopterin biosynthesis moea protein, domain 2 / Molybdopterin biosynthesis moea protein, domain 2 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H. | ||||||
![]() | ![]() Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs. Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 339.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 290.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 474.7 KB | Display | |
Data in XML | ![]() | 32.1 KB | Display | |
Data in CIF | ![]() | 44.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ivyC ![]() 2jg5C ![]() 2jg6C ![]() 2vw8C ![]() 2vxzC ![]() 2wj9C ![]() 2x0oC ![]() 2x3dC ![]() 2x3eC ![]() 2x3fC ![]() 2x3gC ![]() 2x3mC ![]() 2x3nC ![]() 2x3oC ![]() 2x48C ![]() 2x4gC ![]() 2x4hC ![]() 2x4iC ![]() 2x4jC ![]() 2x4kC ![]() 2x4lC ![]() 2x5cC ![]() 2x5dC ![]() 2x5fC ![]() 2x5gC ![]() 2x5hC ![]() 2x5pC ![]() 2x5qC ![]() 2x5rC ![]() 2x5tC ![]() 2x7bC ![]() 2x7iC ![]() 2xu2C C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
|
-
Components
#1: Protein | Mass: 51122.285 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-SM / #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 43 % / Description: NONE |
---|---|
Crystal grow | pH: 8 Details: 20% PEG4000, 0.1 M TRIS-CL, PH8.0, 0.32 M MGCL2, 0.8% ETHYLENE GLYCOL. THE CRYSTAL WAS SOAKED WITH 20 MM SAMARIUM ACETATE AND 5MM PLP. THE CRYSTALS WERE CRYOPROTECTED WITH 22% PEG4000, 0.1M ...Details: 20% PEG4000, 0.1 M TRIS-CL, PH8.0, 0.32 M MGCL2, 0.8% ETHYLENE GLYCOL. THE CRYSTAL WAS SOAKED WITH 20 MM SAMARIUM ACETATE AND 5MM PLP. THE CRYSTALS WERE CRYOPROTECTED WITH 22% PEG4000, 0.1M TRIS-CL, PH8.0, 0.3 M MGCL2, 2.0% ETHYLENE GLYCOL, 19% PEG400 DILUTED WITH A 50MM PLP SOLUTION 1:10 (FINAL CONCENTRATIONS ABOUT 17% PEG400 AND 5MM PLP) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 25, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.17 Å / Num. obs: 50798 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.7 / % possible all: 98.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2→29.17 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.868 / SU B: 14.06 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE IS ONLY ORDERED FROM RESIDUE 5 TO 443. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE IS ONLY ORDERED FROM RESIDUE 5 TO 443. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.754 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.17 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|