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- PDB-4d1t: High resolution structure of native tVIM-7 from Pseudomonas aeruginosa -
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Open data
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Basic information
Entry | Database: PDB / ID: 4d1t | ||||||
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Title | High resolution structure of native tVIM-7 from Pseudomonas aeruginosa | ||||||
![]() | METALLO-B-LACTAMASE | ||||||
![]() | HYDROLASE / RESIDUE DETERMINANTS / LIGAND INTERACTION | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Leiros, H.-K.S. / Skagseth, S. / Edvardsen, K.S.W. / Lorentzen, M.S. / Bjerga, G.E.K. / Leiros, I. / Samuelsen, O. | ||||||
![]() | ![]() Title: His224 Alters the R2 Drug Binding Site and Phe218 Influences the Catalytic Efficiency in the Metallo-Beta-Lactamase Vim-7. Authors: Leiros, H.-K.S. / Skagseth, S. / Edvardsen, K.S.W. / Lorentzen, M.S. / Bjerga, G.E.K. / Leiros, I. / Samuelsen, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.6 KB | Display | ![]() |
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PDB format | ![]() | 125 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.7 KB | Display | ![]() |
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Full document | ![]() | 431.9 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d1uC ![]() 4d1vC ![]() 4d1wC ![]() 2y8bS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28132.877 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.53 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→30 Å / Num. obs: 61189 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.23→1.32 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2 / % possible all: 78.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Y8B Resolution: 1.25→23.326 Å / SU ML: 0.1 / σ(F): 1.34 / Phase error: 13.12 / 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: 14.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→23.326 Å
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Refine LS restraints |
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LS refinement shell |
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