+Open data
-Basic information
Entry | Database: PDB / ID: 5dsf | |||||||||
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Title | Crystal structure of the mercury-bound form of MerB mutant D99S | |||||||||
Components | Alkylmercury lyase | |||||||||
Keywords | LYASE / METAL BINDING PROTEIN | |||||||||
Function / homology | Function and homology information alkylmercury lyase / alkylmercury lyase activity / : / response to mercury ion Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.954 Å | |||||||||
Authors | Wahba, H.M. / Lecoq, L. / Stevenson, M. / Mansour, A. / Cappadocia, L. / Lafrance-Vanasse, J. / Wilkinson, K.J. / Sygusch, J. / Wilcox, D.E. / Omichinski, J.G. | |||||||||
Funding support | Canada, United States, 2items
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Citation | Journal: Biochemistry / Year: 2016 Title: Structural and Biochemical Characterization of a Copper-Binding Mutant of the Organomercurial Lyase MerB: Insight into the Key Role of the Active Site Aspartic Acid in Hg-Carbon Bond Cleavage ...Title: Structural and Biochemical Characterization of a Copper-Binding Mutant of the Organomercurial Lyase MerB: Insight into the Key Role of the Active Site Aspartic Acid in Hg-Carbon Bond Cleavage and Metal Binding Specificity. Authors: Wahba, H.M. / Lecoq, L. / Stevenson, M. / Mansour, A. / Cappadocia, L. / Lafrance-Vanasse, J. / Wilkinson, K.J. / Sygusch, J. / Wilcox, D.E. / Omichinski, J.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dsf.cif.gz | 243.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dsf.ent.gz | 198.2 KB | Display | PDB format |
PDBx/mmJSON format | 5dsf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dsf_validation.pdf.gz | 428.6 KB | Display | wwPDB validaton report |
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Full document | 5dsf_full_validation.pdf.gz | 430.3 KB | Display | |
Data in XML | 5dsf_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 5dsf_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/5dsf ftp://data.pdbj.org/pub/pdb/validation_reports/ds/5dsf | HTTPS FTP |
-Related structure data
Related structure data | 5c0tC 5c0uC 5c17C 3f0oS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23030.258 Da / Num. of mol.: 2 / Mutation: D99S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: merB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77072, alkylmercury lyase #2: Chemical | #3: Chemical | ChemComp-BR / | #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: 1.87 Å3/Da / Density % sol: 34.1 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 23 % polyethylene glycol 2000 MME, 0.2 M sodium acetate pH 5.5, 0.2 M potassium bromide. Before flash freezing, the same precipitant was used except 25 % polyethylene glycol 2000 MME was ...Details: 23 % polyethylene glycol 2000 MME, 0.2 M sodium acetate pH 5.5, 0.2 M potassium bromide. Before flash freezing, the same precipitant was used except 25 % polyethylene glycol 2000 MME was used as a cryo-protectant |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.954→50 Å / Num. obs: 24336 / % possible obs: 99.12 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.07695 / Net I/σ(I): 12.14 |
Reflection shell | Resolution: 1.954→2.024 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5835 / % possible all: 96.81 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F0O Resolution: 1.954→36.996 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 21.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.27 Å2 / Biso mean: 35.626 Å2 / Biso min: 12.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.954→36.996 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27
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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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