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Yorodumi- PDB-4f6h: Mutagenesis of zinc ligand residue Cys221 reveals plasticity in t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f6h | ||||||
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Title | Mutagenesis of zinc ligand residue Cys221 reveals plasticity in the IMP-1 metallo-b-lactamase active site | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / metallo-b-lactamase / b-lactamase | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.744 Å | ||||||
Authors | Horton, L.B. / Shanker, S. / Sankaran, B. / Mikulski, R. / Brown, N.G. / Phillips, K. / Lykissa, E. / Prasad, B.V.V. / Palzkill, T.G. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2012 Title: Mutagenesis of zinc ligand residue Cys221 reveals plasticity in the IMP-1 metallo-beta-lactamase active site Authors: Horton, L.B. / Shanker, S. / Mikulski, R. / Brown, N.G. / Phillips, K.J. / Lykissa, E. / Venkataram Prasad, B.V. / Palzkill, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f6h.cif.gz | 105.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f6h.ent.gz | 81.1 KB | Display | PDB format |
PDBx/mmJSON format | 4f6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4f6h_validation.pdf.gz | 447.6 KB | Display | wwPDB validaton report |
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Full document | 4f6h_full_validation.pdf.gz | 450 KB | Display | |
Data in XML | 4f6h_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 4f6h_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/4f6h ftp://data.pdbj.org/pub/pdb/validation_reports/f6/4f6h | HTTPS FTP |
-Related structure data
Related structure data | 4f6zC 1ddkS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26142.732 Da / Num. of mol.: 1 / Mutation: C176G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaIMP-1, bla IMP, bla-imp, blaESP, imp / Production host: Escherichia coli (E. coli) / References: UniProt: Q79MP6 | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | #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: 2.44 Å3/Da / Density % sol: 49.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25 mMTris-HCl containing 1 mM zinc sulfate at pH 7.0, and mother liquor containing 0.8M di-sodium hydrogen phosphate, 0.8 M di-potassium hydrogen phosphate, and 0.1 M HEPES at pH 7.5., VAPOR ...Details: 25 mMTris-HCl containing 1 mM zinc sulfate at pH 7.0, and mother liquor containing 0.8M di-sodium hydrogen phosphate, 0.8 M di-potassium hydrogen phosphate, and 0.1 M HEPES at pH 7.5., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9774 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→30.25 Å / Num. all: 26059 / Num. obs: 26059 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.036 |
Reflection shell | Resolution: 1.74→1.81 Å / Rmerge(I) obs: 0.306 / % possible all: 89.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1DDK Resolution: 1.744→30.249 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 24.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.717 Å2 / ksol: 0.383 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.744→30.249 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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