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Yorodumi- PDB-3n7w: Crystal Structure of BlaC-E166A covalently bound with Amoxicillin -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n7w | ||||||
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Title | Crystal Structure of BlaC-E166A covalently bound with Amoxicillin | ||||||
Components | Beta-lactamase | ||||||
Keywords | Hydrolase/Antibiotic / penicillin binding protein / beta-lactam covalent adduct / Hydrolase-Antibiotic complex | ||||||
Function / homology | Function and homology information : / : / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Tremblay, L.W. / Blanchard, J.S. | ||||||
Citation | Journal: To be Published Title: BlaC-E166A Bound with btea-lactams of all classes Authors: Tremblay, L.W. / Blanchard, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n7w.cif.gz | 70.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n7w.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 3n7w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n7w_validation.pdf.gz | 799.4 KB | Display | wwPDB validaton report |
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Full document | 3n7w_full_validation.pdf.gz | 800.5 KB | Display | |
Data in XML | 3n7w_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 3n7w_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/3n7w ftp://data.pdbj.org/pub/pdb/validation_reports/n7/3n7w | HTTPS FTP |
-Related structure data
Related structure data | 3dwzS 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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Unit cell |
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-Components
#1: Protein | Mass: 28214.689 Da / Num. of mol.: 1 / Mutation: E182A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: blaA, blaC, MT2128, MTCY49.07c, Rv2068c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 References: UniProt: P0C5C1, UniProt: P9WKD3*PLUS, beta-lactamase | ||
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#2: Chemical | ChemComp-AXL / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES, 2 M NH4H2PO4, pH 7.5, Vapor diffusion, Sitting drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: 2009 |
Radiation | Monochromator: Si(111) Channel Cut / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50.61 Å / Num. all: 29045 / Num. obs: 26464 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.7→1.744 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3391 / % possible all: 80.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3DWZ Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.176 / WRfactor Rwork: 0.148 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.911 / SU B: 1.58 / SU ML: 0.053 / SU R Cruickshank DPI: 0.106 / SU Rfree: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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 max: 52.26 Å2 / Biso mean: 15.027 Å2 / Biso min: 5.74 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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