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Yorodumi- PDB-5mld: Crystal Structure of RosB with bound intermediate AFP (8-demethyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mld | ||||||
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Title | Crystal Structure of RosB with bound intermediate AFP (8-demethyl-8-aminoriboflavin-5'-phosphate) | ||||||
Components | BRAMP domain protein | ||||||
Keywords | ELECTRON TRANSPORT / Flavodoxin-like / roseoflavin / vitamin B2 | ||||||
Function / homology | Function and homology information 8-demethyl-8-aminoriboflavin-5'-phosphate synthase / antibiotic metabolic process / transaminase activity / antibiotic biosynthetic process / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Streptomyces davawensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Konjik, V. / Bruenle, S. / Demmer, U. / Vanselow, A. / Sandhoff, R. / Mack, M. / Ermler, U. | ||||||
Citation | Journal: To be published Title: The crystal structure of RosB gives insights into the reaction mechanism of this first known member of a new family of flavodoxin-like enzymes Authors: Konjik, V. / Bruenle, S. / Demmer, U. / Vanselow, A. / Sandhoff, R. / Mack, M. / Ermler, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mld.cif.gz | 442.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mld.ent.gz | 366 KB | Display | PDB format |
PDBx/mmJSON format | 5mld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mld_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 5mld_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 5mld_validation.xml.gz | 93.4 KB | Display | |
Data in CIF | 5mld_validation.cif.gz | 131.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/5mld ftp://data.pdbj.org/pub/pdb/validation_reports/ml/5mld | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28899.688 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces davawensis (bacteria) / Gene: BN159_7989 / Production host: Escherichia coli (E. coli) / References: UniProt: K4REZ6 #2: Chemical | ChemComp-8DP / #3: 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: 2.17 Å3/Da / Density % sol: 43.34 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion Details: 0.3 M sodium formate, 0.1 M potassium chloride, 17 % (v/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 202389 / % possible obs: 92.9 % / Redundancy: 10.7 % / Rsym value: 0.106 / Net I/σ(I): 15.36 |
-Processing
Software |
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Refinement | Resolution: 1.7→47.54 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.18 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→47.54 Å
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Refine LS restraints |
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LS refinement shell |
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