+
Open data
-
Basic information
Entry | Database: PDB / ID: 8p3a | ||||||
---|---|---|---|---|---|---|---|
Title | bacteriophage T5 l-alanoyl-d-glutamate peptidase Zn2+/Ca2+ form | ||||||
![]() | L-alanyl-D-glutamate peptidase | ||||||
![]() | ANTIMICROBIAL PROTEIN / l-alanoyl-d-glutamate peptidase / bacteriophage T5 / endolysin / Zn2+ and Ca2+ containing form | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metabolic process / viral release from host cell by cytolysis / cell wall organization / peptidase activity / defense response to bacterium / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
![]() | Prokhorov, D.A. / Kutyshenko, V.P. / Mikoulinskaia, G.V. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Mechanism of Ca2+-dependent activation of L-alanoyl-D-glutamate peptidase bacteriophage T5. Authors: Prokhorov, D.A. / Mikoulinskaia, G.V. / Molochkov, N.V. / Uversky, V.N. / Kutyshenko, V.P. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 839.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 705.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 405.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 555.3 KB | Display | |
Data in XML | ![]() | 66.8 KB | Display | |
Data in CIF | ![]() | 80.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
Other databases |
|
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-
Components
#1: Protein | Mass: 15286.202 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ZN - ZN2+ ION CA - CA2+ ION / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q6QGP7, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
---|---|
#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-CA / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-
Sample preparation
Details | Type: solution Contents: 0.8 mM [U-100% 13C; U-100% 15N] l-alanoyl-d-glutamate peptidase, 50 mM [U-100% 2H] sodium acetate, 3 mM Zn(NO3)2, 3 mM CaCl2, 0.03 % sodium azide, 90% H2O/10% D2O Details: The sample was obtained by renaturation from a solution of 8 M urea in the presence of Zn2+ and Ca2+ salts Label: endo_T5 Zn-Ca / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||||||
Sample conditions | Details: The sample remained stable throughout the entire data collection period. The stability of the sample was monitored by periodically recording 15N-HSQC spectra and comparing them. Ionic strength: 50 mM / Ionic strength err: 5 / Label: conditions_1 / pH: 4.1 / PH err: 0.05 / Pressure: AMBIENT atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.2 |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: TXI probehead |
---|
-
Processing
NMR software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: target function | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |