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Yorodumi- PDB-6kby: Crystal structure of a class C beta lactamase in complex with AMP -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kby | ||||||
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Title | Crystal structure of a class C beta lactamase in complex with AMP | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / Crystal structures / Class C beta-lactamase / Acyl-enzyme complex / AMP | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic / nucleotide binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.097 Å | ||||||
Authors | Bae, D.W. / Jung, Y.E. / An, Y.J. / Na, J.H. / Cha, S.S. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2019 Title: Structural Insights into Catalytic Relevances of Substrate Poses in ACC-1. Authors: Bae, D.W. / Jung, Y.E. / An, Y.J. / Na, J.H. / Cha, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kby.cif.gz | 93.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kby.ent.gz | 72.2 KB | Display | PDB format |
PDBx/mmJSON format | 6kby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kby_validation.pdf.gz | 773 KB | Display | wwPDB validaton report |
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Full document | 6kby_full_validation.pdf.gz | 774.7 KB | Display | |
Data in XML | 6kby_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 6kby_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/6kby ftp://data.pdbj.org/pub/pdb/validation_reports/kb/6kby | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40713.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla-ACC-1, acc-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XB24, beta-lactamase |
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#2: Chemical | ChemComp-AMP / |
#3: 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: 2.55 Å3/Da / Density % sol: 51.68 % |
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Crystal grow | Temperature: 295 K / Method: microbatch Details: 0.1M sodium cacodylate pH 5.5, 0.2M sodium chloride, 35% polyethylene glycol 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: May 26, 2019 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.097→41.036 Å / Num. obs: 165696 / % possible obs: 99.32 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.024 / Rrim(I) all: 0.063 / Rsym value: 0.058 / Net I/σ(I): 13.21 |
Reflection shell | Resolution: 1.097→1.102 Å / Num. unique obs: 12228 / Rsym value: 0.694 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.097→41.036 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.13
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 38.99 Å2 / Biso mean: 12.9569 Å2 / Biso min: 5.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.097→41.036 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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