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- PDB-7dtn: Crystal structure of metallo-beta-lactamase IMP-1 mutant (D120E) ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dtn | |||||||||
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Title | Crystal structure of metallo-beta-lactamase IMP-1 mutant (D120E) in complex with citrate. | |||||||||
![]() | Metallo-beta-lactamase type 2 | |||||||||
![]() | HYDROLASE / metallo-beta-lactamase / zinc(II) ion / citrate | |||||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yamaguchi, Y. / Kurosaki, H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structures of Metallo-beta-Lactamase (IMP-1) and Its D120E Mutant in Complexes with Citrate and the Inhibitory Effect of the Benzyl Group in Citrate Monobenzyl Ester. Authors: Yamaguchi, Y. / Kato, K. / Ichimaru, Y. / Jin, W. / Sakai, M. / Abe, M. / Wachino, J.I. / Arakawa, Y. / Miyagi, Y. / Imai, M. / Fukuishi, N. / Yamagata, Y. / Otsuka, M. / Fujita, M. / Kurosaki, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 198.6 KB | Display | ![]() |
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PDB format | ![]() | 155.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 7.1 MB | Display | ![]() |
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Full document | ![]() | 7.2 MB | Display | |
Data in XML | ![]() | 40.9 KB | Display | |
Data in CIF | ![]() | 57.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dtmC ![]() 1dd6S 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25208.699 Da / Num. of mol.: 4 / Mutation: D81E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-FLC / #4: Chemical | ChemComp-AE3 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M citric acid-sodium citrate buffer, 0.2M sodium acetate, PEG4000 30 w/v% |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 89488 / % possible obs: 97.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.85→1.88 Å / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 5 / Num. unique obs: 4327 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1dd6 Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.287 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 70.04 Å2 / Biso mean: 19.461 Å2 / Biso min: 8.68 Å2
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Refinement step | Cycle: final / Resolution: 1.85→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.896 Å / Rfactor Rfree error: 0
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