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Yorodumi- PDB-6k4t: Crystal structure of SMB-1 metallo-beta-lactamase in a complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k4t | ||||||
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Title | Crystal structure of SMB-1 metallo-beta-lactamase in a complex with TSA | ||||||
Components | Metallo-beta-lactamase | ||||||
Keywords | HYDROLASE / metallo-beta-lactamase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Serratia marcescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å | ||||||
Authors | Wachino, J. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2019 Title: 4-Amino-2-Sulfanylbenzoic Acid as a Potent Subclass B3 Metallo-beta-Lactamase-Specific Inhibitor Applicable for Distinguishing Metallo-beta-Lactamase Subclasses. Authors: Wachino, J. / Kanechi, R. / Nishino, E. / Mochizuki, M. / Jin, W. / Kimura, K. / Kurosaki, H. / Arakawa, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k4t.cif.gz | 77.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k4t.ent.gz | 53.6 KB | Display | PDB format |
PDBx/mmJSON format | 6k4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k4t_validation.pdf.gz | 793.5 KB | Display | wwPDB validaton report |
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Full document | 6k4t_full_validation.pdf.gz | 793.5 KB | Display | |
Data in XML | 6k4t_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 6k4t_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/6k4t ftp://data.pdbj.org/pub/pdb/validation_reports/k4/6k4t | HTTPS FTP |
-Related structure data
Related structure data | 5y5bC 6jedC 6k4xC 5b1uS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: SMB-1 / Production host: Escherichia coli (E. coli) / References: UniProt: G5ELM3, beta-lactamase |
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-Non-polymers , 5 types, 438 molecules
#2: Chemical | #3: Chemical | ChemComp-JKE / | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M lithium sulfate, 0.1M Tris-HCl (pH 8.5), 20% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2016 |
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→40.61 Å / Num. obs: 42083 / % possible obs: 90.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.39→1.47 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.077 / Num. unique obs: 5988 / % possible all: 87.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B1U Resolution: 1.39→19.66 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 0.756 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.062 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.343 Å2
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Refinement step | Cycle: 1 / Resolution: 1.39→19.66 Å
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Refine LS restraints |
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