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Yorodumi- PDB-6u2y: Crystal Structure of the metallo-beta-lactamase L1 from Stenotrop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6u2y | ||||||
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Title | Crystal Structure of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the complex with the hydrolyzed moxalactam and two Ni ions | ||||||
Components | Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase) | ||||||
Keywords | HYDROLASE / lactam antibiotics / Moxalactam / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | Stenotrophomonas maltophilia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Kim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the complex with the hydrolyzed moxalactam and two Ni ions Authors: Kim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u2y.cif.gz | 132.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u2y.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 6u2y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6u2y_validation.pdf.gz | 363.3 KB | Display | wwPDB validaton report |
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Full document | 6u2y_full_validation.pdf.gz | 363.2 KB | Display | |
Data in XML | 6u2y_validation.xml.gz | 1.5 KB | Display | |
Data in CIF | 6u2y_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/6u2y ftp://data.pdbj.org/pub/pdb/validation_reports/u2/6u2y | HTTPS FTP |
-Related structure data
Related structure data | 6u0yS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29172.857 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria) Strain: K279a / Gene: Smlt2667 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): gold / References: UniProt: B2FTM1, beta-lactamase | ||||||
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#2: Chemical | ChemComp-MX1 / ( | ||||||
#3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.65 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M Sodium malonate pH 7.0, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 50905 / % possible obs: 99.7 % / Redundancy: 10 % / Biso Wilson estimate: 18.98 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 22.76 |
Reflection shell | Resolution: 1.5→1.53 Å / Rmerge(I) obs: 0.792 / Mean I/σ(I) obs: 1.21 / Num. unique obs: 2426 / CC1/2: 0.701 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDBID 6U0Y Resolution: 1.5→46.07 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 24.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→46.07 Å
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Refine LS restraints |
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LS refinement shell |
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