+Open data
-Basic information
Entry | Database: PDB / ID: 2hdq | ||||||
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Title | AmpC beta-lactamase in complex with 2-carboxythiophene | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / Fragment-based beta-lactamase AmpC drug design | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / 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: 2.1 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 | 2hdq.cif.gz | 161.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hdq.ent.gz | 127 KB | Display | PDB format |
PDBx/mmJSON format | 2hdq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hdq_validation.pdf.gz | 453.3 KB | Display | wwPDB validaton report |
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Full document | 2hdq_full_validation.pdf.gz | 458.3 KB | Display | |
Data in XML | 2hdq_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 2hdq_validation.cif.gz | 46.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/2hdq ftp://data.pdbj.org/pub/pdb/validation_reports/hd/2hdq | HTTPS FTP |
-Related structure data
Related structure data | 2hdrC 2hdsC 2hduC 1ke4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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-C21 / #3: 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: 50.53 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 1.7M potassium phosphate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 8, 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: 2.5 % / Av σ(I) over netI: 7.9 / Number: 101651 / Rmerge(I) obs: 0.089 / Χ2: 1.27 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 41267 / % possible obs: 91 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.1→50 Å / Num. obs: 69905 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 12.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2.2 / % possible all: 78.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KE4 Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.963 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.263 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 18.107 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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