+Open data
-Basic information
Entry | Database: PDB / ID: 1p3y | ||||||
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Title | MrsD from Bacillus sp. HIL-Y85/54728 | ||||||
Components | MrsD protein | ||||||
Keywords | OXIDOREDUCTASE / flavoprotein / FMN / Rossmann fold / HFCD family / oxdidative decarboxylation / cystein / lantibiotics / mersacidin | ||||||
Function / homology | Function and homology information Lyases; Carbon-carbon lyases; Carboxy-lyases / antibiotic biosynthetic process / oxidoreductase activity / lyase activity Similarity search - Function | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å | ||||||
Authors | Blaesse, M. / Kupke, T. / Huber, R. / Steinbacher, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Structure of MrsD, an FAD-binding protein of the HFCD family. Authors: Blaesse, M. / Kupke, T. / Huber, R. / Steinbacher, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p3y.cif.gz | 51.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p3y.ent.gz | 37.2 KB | Display | PDB format |
PDBx/mmJSON format | 1p3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/1p3y ftp://data.pdbj.org/pub/pdb/validation_reports/p3/1p3y | HTTPS FTP |
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-Related structure data
Related structure data | 1g5qS 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: 21708.256 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: HIL-Y85/54728 / Gene: mrsD / Plasmid: pQE12 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9RC23 |
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#2: Chemical | ChemComp-FAD / |
#3: 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: 3.59 Å3/Da / Density % sol: 65.48 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.1 Details: KNa tartrate, pH 9.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 12, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→20 Å / Num. all: 10384 / Num. obs: 10384 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 2.54→2.68 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 5.4 / % possible all: 99.5 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 99.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1G5Q Resolution: 2.54→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.54→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.222 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |