+Open data
-Basic information
Entry | Database: PDB / ID: 2y2b | ||||||
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Title | crystal structure of AmpD in complex with reaction products | ||||||
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 / peptidoglycan turnover / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 2y2b.cif.gz | 131.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y2b.ent.gz | 101.7 KB | Display | PDB format |
PDBx/mmJSON format | 2y2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y2b_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2y2b_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2y2b_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 2y2b_validation.cif.gz | 43.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/2y2b ftp://data.pdbj.org/pub/pdb/validation_reports/y2/2y2b | HTTPS FTP |
-Related structure data
Related structure data | 2y28SC 2y2cC 2y2dC 2y2eC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 20871.361 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CITROBACTER FREUNDII (bacteria) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P82974, N-acetylmuramoyl-L-alanine amidase #2: Chemical | ChemComp-AH0 / | #3: Chemical | ChemComp-MHI / | #4: Chemical | #5: 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: 0.1M TRIS PH 6.0, 0.1M LI2SO4, 28% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97627 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97627 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 31507 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.9→2.03 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.8 / % possible all: 77 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y28 Resolution: 1.9→50 Å / SU ML: 0.22 / σ(F): 0.02 / Phase error: 23.05 / Stereochemistry target values: ML / Details: LIGANDS WERE FOUND IN MOLECULE A
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.809 Å2 / ksol: 0.386 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell |
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