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Yorodumi- PDB-2ffy: AmpC beta-lactamase N289A mutant in complex with a boronic acid d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ffy | ||||||
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Title | AmpC beta-lactamase N289A mutant in complex with a boronic acid deacylation transition state analog compound SM3 | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / AmpC / beta-lactamase / deacylation / transition state / boronic acid | ||||||
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 / SYNCHROTRON / AB INITIO / Resolution: 1.07 Å | ||||||
Authors | Chen, Y. / Minasov, G. / Roth, T.A. / Prati, F. / Shoichet, B.K. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2006 Title: The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution Authors: Chen, Y. / Minasov, G. / Roth, T.A. / Prati, F. / 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 | 2ffy.cif.gz | 508.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ffy.ent.gz | 428.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ffy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/2ffy ftp://data.pdbj.org/pub/pdb/validation_reports/ff/2ffy | HTTPS FTP |
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-Related structure data
Related structure data | 1pi4S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Each asymmetric unit contains two protein monomers. The protein functions as a monomer |
-Components
#1: Protein | Mass: 39544.898 Da / Num. of mol.: 2 / Mutation: N289A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ampC, ampA / Plasmid: POGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase #2: Chemical | #3: Chemical | #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: 2.52 Å3/Da / Density % sol: 51.11 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: POTASSIUM PHOSPHATE BUFFER, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.97014 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 4, 2003 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97014 Å / Relative weight: 1 |
Reflection | Resolution: 1.07→15 Å / Num. all: 325964 / Num. obs: 325964 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 12.07 |
Reflection shell | Resolution: 1.07→1.11 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2.34 / Num. unique all: 30545 / % possible all: 85.7 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: 1PI4 Resolution: 1.07→15 Å / Num. parameters: 69096 / Num. restraintsaints: 103348 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER Details: Heavy atoms were refined anisotropically. Riding hydrogen atoms on protein C atoms and backbone N atoms were added by Shelx automatically. Hydrogen atoms on -OH groups of SER, THR and TYR ...Details: Heavy atoms were refined anisotropically. Riding hydrogen atoms on protein C atoms and backbone N atoms were added by Shelx automatically. Hydrogen atoms on -OH groups of SER, THR and TYR were modeled when corresponding positive peaks were observed above 1.5 sigma level in hydrogen-omitted Fo-Fc map. Hydrogen atoms positions remained fixed relative to the heavy atoms during refinement.
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Refine analyze | Num. disordered residues: 279 / Occupancy sum hydrogen: 5291.28 / Occupancy sum non hydrogen: 6570.99 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.07→15 Å
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Refine LS restraints |
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