+Open data
-Basic information
Entry | Database: PDB / ID: 4bj4 | ||||||
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Title | Structure of Pseudomonas aeruginosa amidase Ampdh2 | ||||||
Components | AMPDH2 | ||||||
Keywords | HYDROLASE / PERIPLASMIC AMIDASE | ||||||
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 / metal ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.722 Å | ||||||
Authors | Martinez-Caballero, C.S. / Carrasco-Lopez, C. / Artola-Recolons, C. / Hermoso, J.A. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2013 Title: Reaction Products and the X-Ray Structure of Ampdh2, a Virulence Determinant of Pseudomonas Aeruginosa. Authors: Martinez-Caballero, S. / Lee, M. / Artola-Recolons, C. / Carrasco-Lopez, C. / Hesek, D. / Spink, E.E. / Lastochkin, E. / Zhang, W. / Hellman, L.M. / Boggess, B. / 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 | 4bj4.cif.gz | 129.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bj4.ent.gz | 99.8 KB | Display | PDB format |
PDBx/mmJSON format | 4bj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bj4_validation.pdf.gz | 448 KB | Display | wwPDB validaton report |
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Full document | 4bj4_full_validation.pdf.gz | 450.6 KB | Display | |
Data in XML | 4bj4_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 4bj4_validation.cif.gz | 45.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/4bj4 ftp://data.pdbj.org/pub/pdb/validation_reports/bj/4bj4 | HTTPS FTP |
-Related structure data
Related structure data | 4bolC 4bpaC 2wkxS 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
#1: Protein | Mass: 27496.998 Da / Num. of mol.: 2 / Fragment: RESIDUES 18-259 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(DE3) References: UniProt: Q9HT86, N-acetylmuramoyl-L-alanine amidase #2: Chemical | ChemComp-FLC / | #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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 5.1 Details: 0.2 M POTASSIUM THIOCYANATE, 0.1 M BIS-TRIS PROPANE PH 7.5, 18 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 1.00002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→48.76 Å / Num. obs: 54928 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.72→1.81 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 5.2 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WKX Resolution: 1.722→46.267 Å / SU ML: 0.21 / σ(F): 1.33 / Phase error: 19.9 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.722→46.267 Å
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Refine LS restraints |
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LS refinement shell |
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