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- PDB-4rl2: Structural and mechanistic insights into NDM-1 catalyzed hydrolys... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rl2 | ||||||
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Title | Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins | ||||||
![]() | Beta-lactamase NDM-1 | ||||||
![]() | HYDROLASE / NDM-1 antibiotic hydrolysis | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Feng, H. / Ding, J. / Zhu, D. / Liu, X. / Xu, X. / Zhang, Y. / Zang, S. / Wang, D.-C. / Liu, W. | ||||||
![]() | ![]() Title: Structural and Mechanistic Insights into NDM-1 Catalyzed Hydrolysis of Cephalosporins. Authors: Feng, H. / Ding, J. / Zhu, D. / Liu, X. / Xu, X. / Zhang, Y. / Zang, S. / 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 | ![]() | 115.7 KB | Display | ![]() |
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PDB format | ![]() | 87.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 24.2 KB | Display | |
Data in CIF | ![]() | 35.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rl0C ![]() 4rm5C ![]() 3q6x 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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Unit cell |
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Components
#1: Protein | Mass: 26045.295 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.34 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 28% (w/v) PEG3350, 0.1 M Bis-Tris, pH 5.8 and 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 18, 2012 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.008→38.785 Å / Num. all: 26996 / Num. obs: 26843 / % possible obs: 99.43 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.008→2.12 Å / % possible all: 92.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3Q6X ![]() 3q6x Resolution: 2.008→38.785 Å / SU ML: 0.17 / σ(F): 1.38 / Phase error: 17.17 / 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: 2.008→38.785 Å
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Refine LS restraints |
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LS refinement shell |
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