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- PDB-5ypl: Crystal structure of NDM-1 bound to hydrolyzed imipenem represent... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ypl | ||||||
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Title | Crystal structure of NDM-1 bound to hydrolyzed imipenem representing an EP complex | ||||||
![]() | Metallo-beta-lactamase NDM-1 | ||||||
![]() | HYDROLASE / NDM-1 / Imipenem / EP complex | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Feng, H. / Wang, D. / Liu, W. | ||||||
![]() | ![]() Title: The mechanism of NDM-1-catalyzed carbapenem hydrolysis is distinct from that of penicillin or cephalosporin hydrolysis. Authors: Feng, H. / Liu, X. / Wang, S. / Fleming, J. / Wang, D.C. / Liu, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 191.9 KB | Display | ![]() |
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PDB format | ![]() | 150.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 941.8 KB | Display | ![]() |
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Full document | ![]() | 944.3 KB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 33.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ypiC ![]() 5ypkC ![]() 5ypmC ![]() 5ypnC ![]() 4rl0S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25631.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 379 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/HIW.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HIW.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.2 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 28% (w/v) PEG3350, 0.1M Bis-Tris, pH 5.8, 0.2M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97845 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→42.28 Å / Num. obs: 35229 / % possible obs: 94 % / Redundancy: 6.36 % / Rsym value: 0.07 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 4.44 % / Mean I/σ(I) obs: 2.55 / Rsym value: 0.555 / % possible all: 64.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4RL0 Resolution: 1.8→42.28 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.73 Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→42.28 Å
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