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- PDB-5axo: Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrol... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5axo | ||||||
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Title | Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Meropenem | ||||||
![]() | Metallo-beta-lactamase | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wachino, J. / Arakawa, Y. | ||||||
![]() | ![]() Title: Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Meropenem Authors: Wachino, J. / Arakawa, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77 KB | Display | ![]() |
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PDB format | ![]() | 53.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 835.3 KB | Display | ![]() |
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Full document | ![]() | 835.5 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vpeS ![]() 5awy 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27754.043 Da / Num. of mol.: 1 / Fragment: UNP residues 19-280 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 359 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/LMP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/LMP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | #5: Chemical | ChemComp-TRS / | #6: Chemical | ChemComp-LMP / ( | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 42.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, Lithium sulfate, Tris-Hydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→40.62 Å / Num. obs: 39458 / % possible obs: 86.2 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.39→1.47 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.063 / Mean I/σ(I) obs: 1.9 / % possible all: 86 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VPE Resolution: 1.39→40.62 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.721 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.715 Å2
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Refinement step | Cycle: LAST / Resolution: 1.39→40.62 Å
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Refine LS restraints |
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