+Open data
-Basic information
Entry | Database: PDB / ID: 4bxj | |||||||||
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Title | CRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA | |||||||||
Components | AMPDH3 | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information N-acetylmuramoyl-L-alanine amidase / Gram-negative-bacterium-type cell wall / peptidoglycan turnover / N-acetylmuramoyl-L-alanine amidase activity / outer membrane / peptidoglycan catabolic process / cell wall organization / metal ion binding Similarity search - Function | |||||||||
Biological species | PSEUDOMONAS AERUGINOSA PAO1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | |||||||||
Authors | Carrasco-Lopez, C. / Hermoso, J.A. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2013 Title: Cell-Wall Remodeling by the Zinc-Protease Ampdh3 from Pseudomonas Aeruginosa. Authors: Lee, M. / Artola-Recolons, C. / Carrasco-Lopez, C. / Martinez-Caballero, S. / Hesek, D. / Spink, E. / Lastochkin, E. / Zhang, W. / Hellman, L.M. / Boggess, B. / Hermoso, J.A. / Mobashery, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bxj.cif.gz | 117.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bxj.ent.gz | 92.5 KB | Display | PDB format |
PDBx/mmJSON format | 4bxj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/4bxj ftp://data.pdbj.org/pub/pdb/validation_reports/bx/4bxj | HTTPS FTP |
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-Related structure data
Related structure data | 4bxdC 4bxeC 4bj4S 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28756.244 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q9I5D1, N-acetylmuramoyl-L-alanine amidase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.38 % / Description: NONE |
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Crystal grow | pH: 4.5 / Details: pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→48.63 Å / Num. obs: 36822 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 42.6 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 5.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BJ4 Resolution: 2.35→48.627 Å / SU ML: 0.41 / σ(F): 1.33 / Phase error: 29.92 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→48.627 Å
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Refine LS restraints |
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LS refinement shell |
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