- PDB-4axv: Biochemical and structural characterization of the MpaA amidase a... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 4axv
Title
Biochemical and structural characterization of the MpaA amidase as part of a conserved scavenging pathway for peptidoglycan derived peptides in gamma-proteobacteria
Components
MPAA
Keywords
HYDROLASE
Function / homology
Function and homology information
murein tripeptide carboxypeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / peptidoglycan catabolic process / cell wall organization / cell wall macromolecule catabolic process / zinc ion binding / cytoplasm Similarity search - Function
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9797 Å / Relative weight: 1
Reflection
Resolution: 2.17→69.57 Å / Num. obs: 18606 / % possible obs: 100 % / Observed criterion σ(I): 7.4 / Redundancy: 40.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 33.5
Reflection shell
Resolution: 2.17→2.23 Å / Redundancy: 42.7 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 7.4 / % possible all: 100
-
Processing
Software
Name
Version
Classification
REFMAC
5.7.0025
refinement
xia2
datareduction
xia2
datascaling
SHELX
CDE
phasing
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 2.17→60.96 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.426 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23293
948
5.1 %
RANDOM
Rwork
0.19572
-
-
-
obs
0.19761
17580
99.99 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK