[English] 日本語
Yorodumi- PDB-3f0p: Crystal structure of the mercury-bound form of MerB, the Organome... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f0p | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the mercury-bound form of MerB, the Organomercurial Lyase involved in a bacterial mercury resistance system | ||||||
Components | Alkylmercury lyase | ||||||
Keywords | LYASE / merb / organomercurial lyase / alkylmercury lyase / mercury resistance / PHMBA / Mercuric resistance / Plasmid | ||||||
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: 1.64 Å | ||||||
Authors | Lafrance-Vanasse, J. / Lefebvre, M. / Di Lello, P. / Sygusch, J. / Omichinski, J.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Crystal Structures of the Organomercurial Lyase MerB in Its Free and Mercury-bound Forms: INSIGHTS INTO THE MECHANISM OF METHYLMERCURY DEGRADATION Authors: Lafrance-Vanasse, J. / Lefebvre, M. / Di Lello, P. / Sygusch, J. / Omichinski, J.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3f0p.cif.gz | 95.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3f0p.ent.gz | 72.1 KB | Display | PDB format |
PDBx/mmJSON format | 3f0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f0p_validation.pdf.gz | 435.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3f0p_full_validation.pdf.gz | 438 KB | Display | |
Data in XML | 3f0p_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 3f0p_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/3f0p ftp://data.pdbj.org/pub/pdb/validation_reports/f0/3f0p | HTTPS FTP |
-Related structure data
Related structure data | 3f0oSC 3f2fC 3f2gC 3f2hC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23058.268 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: merB / Plasmid: pET21b / 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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.66 % |
---|---|
Crystal grow | Temperature: 296 K / pH: 5.5 Details: 20% polyethylene glycol 2000 MME, 0.2 M sodium acetate pH 5.5, 0.2 M potassium bromide , VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 21, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→20 Å / Num. obs: 40293 / % possible obs: 96.6 % / Redundancy: 3.9 % / Rsym value: 0.064 |
Reflection shell | Resolution: 1.64→1.7 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.481 / % possible all: 93.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3F0O Resolution: 1.64→19.47 Å / SU ML: 0.18 / σ(F): 0.07 / Phase error: 20.08 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.2 Å2 / ksol: 0.37 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→19.47 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|