+Open data
-Basic information
Entry | Database: PDB / ID: 2y28 | ||||||
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Title | crystal structure of Se-Met AmpD derivative | ||||||
Components | 1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD | ||||||
Keywords | HYDROLASE / PEPTIDOGLYCAN AMIDASE / AMIDASE_2 FAMILY / ACTIVATION MECHANISM | ||||||
Function / homology | Function and homology information N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / cell wall organization / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | CITROBACTER FREUNDII (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y28.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y28.ent.gz | 104.2 KB | Display | PDB format |
PDBx/mmJSON format | 2y28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/2y28 ftp://data.pdbj.org/pub/pdb/validation_reports/y2/2y28 | HTTPS FTP |
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-Related structure data
-Links
-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.) CITROBACTER FREUNDII (bacteria) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P82974, N-acetylmuramoyl-L-alanine amidase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97856, 0.978910, 0.918400 | ||||||||||||
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 |
-Processing
Software |
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Refinement | Method to determine structure: MAD 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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