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- PDB-2nyq: Structure of Vibrio proteolyticus aminopeptidase with a bound Trp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2nyq | ||||||
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Title | Structure of Vibrio proteolyticus aminopeptidase with a bound Trp fragment of dLWCF | ||||||
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![]() | HYDROLASE / Trp / VpAP / non-covalent | ||||||
Function / homology | ![]() bacterial leucyl aminopeptidase / metalloexopeptidase activity / aminopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Bennett, B. / Kumar, A. / Narayanan, B. / Kim, J.-J. | ||||||
![]() | ![]() Title: Substrate recognition by the leucine aminopeptidase from Vibrio proteolyticus Authors: Kumar, A. / Narayanan, B. / Kim, J.-J. / Bennett, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72 KB | Display | ![]() |
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PDB format | ![]() | 53.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.6 KB | Display | ![]() |
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Full document | ![]() | 433.7 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 20.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1cp6S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32238.150 Da / Num. of mol.: 1 / Fragment: Bacterial leucyl aminopeptidase, residues 97-405 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q01693, bacterial leucyl aminopeptidase | ||
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#2: Protein/peptide | Mass: 567.699 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The tetrapeptide was chemically synthesised using solid-phase manual synthesis via Fmoc-derivatized amino acids, on Rink-amide resin. Source: (synth.) synthetic construct (others) | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.67 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 5 d., 10/100/100 mM KSCN, 0.4/4.5/4.5 M NaCl, 10/100 mM Tris/100 mM Tricine, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 1, 2005 / Details: CONFOCAL |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 12122 / Num. obs: 12122 / % possible obs: 98.4 % / Biso Wilson estimate: 36.5 Å2 / Rsym value: 0.048 |
Reflection shell | Resolution: 2.5→2.59 Å / Rsym value: 0.139 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1CP6 Resolution: 2.5→50 Å
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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