+Open data
-Basic information
Entry | Database: PDB / ID: 8p3a | ||||||
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Title | bacteriophage T5 l-alanoyl-d-glutamate peptidase Zn2+/Ca2+ form | ||||||
Components | L-alanyl-D-glutamate peptidase | ||||||
Keywords | ANTIMICROBIAL PROTEIN / l-alanoyl-d-glutamate peptidase / bacteriophage T5 / endolysin / Zn2+ and Ca2+ containing form | ||||||
Function / homology | Function and homology information 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 | Escherichia phage T5 (virus) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Prokhorov, D.A. / Kutyshenko, V.P. / Mikoulinskaia, G.V. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: To Be Published 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p3a.cif.gz | 835.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p3a.ent.gz | 705.3 KB | Display | PDB format |
PDBx/mmJSON format | 8p3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/8p3a ftp://data.pdbj.org/pub/pdb/validation_reports/p3/8p3a | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-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.) Escherichia phage T5 (virus) / Gene: lys, T5.040, T5p039, orf10c / Production host: Escherichia coli B (bacteria) References: UniProt: Q6QGP7, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-CA / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-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 | ||||||||||||||||||||||||
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Sample |
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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 |
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-Processing
NMR software |
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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 |