+Open data
-Basic information
Entry | Database: PDB / ID: 3bmz | ||||||
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Title | Violacein biosynthetic enzyme VioE | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | BIOSYNTHETIC PROTEIN / violacein | ||||||
Function / homology | Function and homology information outer membrane lipoprotein receptor (LolB), chain A - #30 / Violacein biosynthesis enzyme, VioE / VioE superfamily / VioE domain / Violacein biosynthetic enzyme VioE / outer membrane lipoprotein receptor (LolB), chain A / Clam / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Chromobacterium violaceum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.21 Å | ||||||
Authors | Ryan, K.S. / Drennan, C.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: The Violacein Biosynthetic Enzyme VioE Shares a Fold with Lipoprotein Transporter Proteins Authors: Ryan, K.S. / Balibar, C.J. / Turo, K.E. / Walsh, C.T. / Drennan, C.L. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bmz.cif.gz | 191.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bmz.ent.gz | 154.1 KB | Display | PDB format |
PDBx/mmJSON format | 3bmz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bmz_validation.pdf.gz | 452 KB | Display | wwPDB validaton report |
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Full document | 3bmz_full_validation.pdf.gz | 455 KB | Display | |
Data in XML | 3bmz_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 3bmz_validation.cif.gz | 36.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/3bmz ftp://data.pdbj.org/pub/pdb/validation_reports/bm/3bmz | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22876.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Strain: ATCC 12472 / Gene: VioE / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) PlysS / References: UniProt: Q7NSZ5 #2: Chemical | ChemComp-PG4 / | #3: Chemical | ChemComp-PGE / | #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: 2.19 Å3/Da / Density % sol: 43.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% (v/v) PEG-400, 20% (w/v) PEG-3350, 0.1 M magnesium chloride, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 141.6 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.21→50 Å / Num. all: 111465 / Num. obs: 111465 / % possible obs: 90.6 % / Redundancy: 13.9 % / Rsym value: 0.066 / Net I/σ(I): 35.7 |
Reflection shell | Resolution: 1.21→1.25 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 6598 / Rsym value: 0.258 / % possible all: 54.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.21→45.31 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.088 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.818 Å2
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Refinement step | Cycle: LAST / Resolution: 1.21→45.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.21→1.241 Å / Total num. of bins used: 20
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