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Yorodumi- PDB-5kmw: TOHO1 Beta lactamase mutant E166A/R274N/R276N -benzyl penicillin ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kmw | ||||||
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Title | TOHO1 Beta lactamase mutant E166A/R274N/R276N -benzyl penicillin complex | ||||||
Components | Beta-lactamase Toho-1 | ||||||
Keywords | HYDROLASE / Class A beta-lactamase / substrate recognition / acyl-enzyme | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Coates, L. / Langan, P.S. / Vandavasi, V.G. / Weiss, K.L. / Cooper, J.B. / Ginell, S.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: to be published Title: TOHO1 Beta lactamase mutant E166A/R274N/R276N -benzyl penicillin complex Authors: Coates, L. / Langan, P.S. / Vandavasi, V.G. / Weiss, K.L. / Cooper, J.B. / Ginell, S.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kmw.cif.gz | 136.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kmw.ent.gz | 110.3 KB | Display | PDB format |
PDBx/mmJSON format | 5kmw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kmw_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5kmw_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5kmw_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 5kmw_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/5kmw ftp://data.pdbj.org/pub/pdb/validation_reports/km/5kmw | HTTPS FTP |
-Related structure data
Related structure data | 5u2x 5u2y 5u2z |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 27503.123 Da / Num. of mol.: 1 / Mutation: E165A, R271N, R273N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla / Production host: Escherichia coli (E. coli) / References: UniProt: Q47066, beta-lactamase | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PNM / | #4: Chemical | #5: 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: 2.69 Å3/Da / Density % sol: 54.29 % |
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Crystal grow | Temperature: 293.15 K / Method: batch mode / pH: 6.1 Details: 30 microliters of 10 mg/ml protein concentration was added to a solution containing 2.0 M ammonium sulfate and 0.1 M sodium citrate (pH 6.1). For ligand soaking, crystals were placed for 2-3 ...Details: 30 microliters of 10 mg/ml protein concentration was added to a solution containing 2.0 M ammonium sulfate and 0.1 M sodium citrate (pH 6.1). For ligand soaking, crystals were placed for 2-3 h in a reservoir solution containing 2.7 M ammonium sulfate, 0.1 M sodium citrate (pH 6.1), and 5.0 mM benzyl penicillin. The crystals were then placed momentarily in a reservoir solution containing a cryoprotectant (30% w/v trehalose) and subsequently flash-frozen in liquid nitrogen |
-Data collection
Diffraction | Mean temperature: 15 K Ambient temp details: Cryo industries of America cryocool Helium cryostream |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.67 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.67 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→38.62 Å / Num. obs: 118234 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 1.1→1.16 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.1 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→10 Å / Num. parameters: 23165 / Num. restraintsaints: 28142 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 19 / Occupancy sum non hydrogen: 2443.8 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.1→10 Å
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Refine LS restraints |
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