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Yorodumi- PDB-1kdw: X-ray crystal structure of AmpC beta-lactamase from E. coli in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kdw | ||||||
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Title | X-ray crystal structure of AmpC beta-lactamase from E. coli in complex with the inhibitor 4-carboxyphenylboronic acid | ||||||
Components | beta-lactamase | ||||||
Keywords | HYDROLASE / cephalosporinase / beta-lactamase / serine hydrolase / phenylboronic acid inhibitor | ||||||
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 (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Powers, R.A. / Shoichet, B.K. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2002 Title: Structure-based approach for binding site identification on AmpC beta-lactamase. Authors: Powers, R.A. / 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 | 1kdw.cif.gz | 152.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kdw.ent.gz | 120.2 KB | Display | PDB format |
PDBx/mmJSON format | 1kdw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kdw_validation.pdf.gz | 464.1 KB | Display | wwPDB validaton report |
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Full document | 1kdw_full_validation.pdf.gz | 474 KB | Display | |
Data in XML | 1kdw_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 1kdw_validation.cif.gz | 42.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/1kdw ftp://data.pdbj.org/pub/pdb/validation_reports/kd/1kdw | HTTPS FTP |
-Related structure data
Related structure data | 1kdsC 1ke0C 1ke3C 1ke4C 1c3bS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39587.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: K12 / Plasmid: pOGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase #2: Chemical | ChemComp-PO4 / | #3: Chemical | #4: 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: 2.55 Å3/Da / Density % sol: 51.71 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 1.7 M potassium phosphate, 485 uM 4-carboxyphenylboronic acid, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / Details: used microseeding | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→20 Å / Num. all: 36794 / Num. obs: 33450 / % possible obs: 91 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 25.46 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.28→2.37 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.5 / % possible all: 62.6 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 90630 / Rmerge(I) obs: 0.075 |
Reflection shell | *PLUS % possible obs: 62.6 % / Rmerge(I) obs: 0.19 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1C3B Resolution: 2.28→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.28→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.28→2.37 Å
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.186 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.345 / Rfactor Rwork: 0.252 |