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Open data
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Basic information
Entry | Database: PDB / ID: 2y28 | ||||||
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Title | crystal structure of Se-Met AmpD derivative | ||||||
![]() | 1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD | ||||||
![]() | HYDROLASE / PEPTIDOGLYCAN AMIDASE / AMIDASE_2 FAMILY / ACTIVATION MECHANISM | ||||||
Function / homology | ![]() N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan turnover / peptidoglycan catabolic process / cell wall organization / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Carrasco-Lopez, C. / Rojas-Altuve, A. / Zhang, W. / Hesek, D. / Lee, M. / Barbe, S. / Andre, I. / Silva-Martin, N. / Martinez-Ripoll, M. / Mobashery, S. / Hermoso, J.A. | ||||||
![]() | ![]() Title: Crystal Structures of Bacterial Peptidoglycan Amidase Ampd and an Unprecedented Activation Mechanism. Authors: Carrasco-Lopez, C. / Rojas-Altuve, A. / Zhang, W. / Hesek, D. / Lee, M. / Barbe, S. / Andre, I. / Ferrer, P. / Silva-Martin, N. / Castro, G.R. / Martinez-Ripoll, M. / Mobashery, S. / Hermoso, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.7 KB | Display | ![]() |
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PDB format | ![]() | 104.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.6 KB | Display | ![]() |
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Full document | ![]() | 453.9 KB | Display | |
Data in XML | ![]() | 29.2 KB | Display | |
Data in CIF | ![]() | 44.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21012.045 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: SE-MET DERIVATIVE / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P82974, N-acetylmuramoyl-L-alanine amidase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 37 % / Description: NONE |
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Crystal grow | pH: 6 / Details: 0.1 M TRIS PH 6.0, 0.1 M LI2SO4, 28% PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 15, 2009 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→58.62 Å / Num. obs: 42178 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 15.89 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16 | ||||||||||||
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.6 / % possible all: 76 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.8→58.624 Å / SU ML: 0.24 / σ(F): 2 / Phase error: 22.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.206 Å2 / ksol: 0.364 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→58.624 Å
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Refine LS restraints |
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LS refinement shell |
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