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Yorodumi- PDB-2hdu: AmpC beta-lactamase in complex with 2-acetamidothiophene-3-carbox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hdu | ||||||
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Title | AmpC beta-lactamase in complex with 2-acetamidothiophene-3-carboxylic acid | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / AmpC beta-lactamase fragment-based drug design | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase / beta-lactamase activity / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Babaoglu, K. / Shoichet, B.K. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2006 Title: Deconstructing fragment-based inhibitor discovery Authors: Babaoglu, K. / Shoichet, B.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hdu.cif.gz | 335.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hdu.ent.gz | 283.9 KB | Display | PDB format |
PDBx/mmJSON format | 2hdu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/2hdu ftp://data.pdbj.org/pub/pdb/validation_reports/hd/2hdu | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | The biological unit is a monomer |
-Components
#1: Protein | Mass: 39587.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: ampC / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase #2: Chemical | ChemComp-F12 / #3: Chemical | ChemComp-K / | #4: Chemical | ChemComp-PO4 / | #5: 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: 2.49 Å3/Da / Density % sol: 50.68 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 14, 2005 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 2.8 % / Av σ(I) over netI: 14.6 / Number: 355860 / Rmerge(I) obs: 0.042 / Χ2: 1 / D res high: 1.49 Å / D res low: 50 Å / Num. obs: 126514 / % possible obs: 99.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.49→50 Å / Num. all: 126514 / Num. obs: 126514 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.042 / Χ2: 0.996 / Net I/σ(I): 14.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.49→1.54 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.3 / Num. unique all: 12573 / Χ2: 0.678 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→87.04 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.061 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.49→87.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.49→1.528 Å / Total num. of bins used: 20
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