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- PDB-3d2z: Complex of the N-acetylmuramyl-L-alanine amidase AmiD from E.coli... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3d2z | ||||||
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Title | Complex of the N-acetylmuramyl-L-alanine amidase AmiD from E.coli with the product L-Ala-D-gamma-Glu-L-Lys | ||||||
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![]() | HYDROLASE / ZINC AMIDASE / PGRP / Peptidoglycan Recognizing Protein / AmpD / N-ACETYLMURAMYL-L-ALANINE AMIDASE / Cell wall biogenesis/degradation / Lipoprotein / Membrane / Metal-binding / Outer membrane / Palmitate | ||||||
Function / homology | ![]() N-acetyl-anhydromuramoyl-L-alanine amidase activity / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan turnover / outer membrane / peptidoglycan catabolic process / cell outer membrane / cell wall organization / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kerff, F. / Petrella, S. / Herman, R. / Sauvage, E. / Mercier, F. / Luxen, A. / Frere, J.M. / Joris, B. / Charlier, P. | ||||||
![]() | ![]() Title: Specific Structural Features of the N-Acetylmuramoyl-l-Alanine Amidase AmiD from Escherichia coli and Mechanistic Implications for Enzymes of This Family. Authors: Kerff, F. / Petrella, S. / Mercier, F. / Sauvage, E. / Herman, R. / Pennartz, A. / Zervosen, A. / Luxen, A. / Frere, J.M. / Joris, B. / Charlier, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67 KB | Display | ![]() |
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PDB format | ![]() | 49.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.4 KB | Display | ![]() |
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Full document | ![]() | 439.8 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 17 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bh7C ![]() 2wkxC ![]() 3d2yC ![]() 2bgx C: citing same article ( 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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2 | ![]()
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Unit cell |
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Details | The biological assembly is a monomer but the protein is found as a dimer in the crystal with a swapping of the N-terminus |
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Components
#1: Protein | Mass: 29376.240 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K-12 MG1655 / Gene: amiD, ybjR, b0867, JW0851 / Plasmid: pBAD/Myc-HisA / Production host: ![]() ![]() References: UniProt: P75820, N-acetylmuramoyl-L-alanine amidase | ||||
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#2: Protein/peptide | Mass: 347.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized | ||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 1M LICL, 10 % PEG 6K, 0.1M ZNCL2, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 20, 2007 |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→47.9 Å / Num. obs: 11312 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.4 % / Rmerge(I) obs: 0.263 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 21 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1592 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BGX ![]() 2bgx Resolution: 2.8→47.9 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.859 / SU B: 13.913 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.582 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.079 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→47.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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