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Yorodumi- PDB-2mxz: Bacteriophage T5 l-alanoyl-d-glutamate peptidase comlpex with Zn2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mxz | ||||||
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Title | Bacteriophage T5 l-alanoyl-d-glutamate peptidase comlpex with Zn2+ (Endo T5-ZN2+) | ||||||
Components | L-alanyl-D-glutamate peptidase | ||||||
Keywords | HYDROLASE / bacteriophage T5 / endolysin / l-alanoyl-d-glutamate peptidase / Zn-containing | ||||||
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 | Enterobacteria phage T5 (virus) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Prokhorov, D.A. / Mikoulinskaia, G.V. / Kutyshenko, V.P. | ||||||
Citation | Journal: RSC ADV / Year: 2015 Title: High-resolution NMR structure of a Zn2+-containing form of the bacteriophage T5 L-alanyl-D-glutamate peptidase 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 | 2mxz.cif.gz | 837 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mxz.ent.gz | 696.4 KB | Display | PDB format |
PDBx/mmJSON format | 2mxz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/2mxz ftp://data.pdbj.org/pub/pdb/validation_reports/mx/2mxz | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-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 Source: (gene. exp.) Enterobacteria phage T5 (virus) / Gene: lys, T5.040, T5p039 / Production host: Escherichia coli (E. coli) References: UniProt: Q6QGP7, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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#2: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR / Details: bacteriophage T5 l-alanoyl-d-glutamate peptidase | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.8 mM [U-100% 13C; U-100% 15N] l-alanoyl-d-glutamate peptidase, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.8 mM / Component: l-alanoyl-d-glutamate peptidase-1 / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: 0.05 / pH: 4.1 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||
NMR constraints | NOE constraints total: 1869 / NOE intraresidue total count: 393 / NOE long range total count: 690 / NOE medium range total count: 299 / NOE sequential total count: 487 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |