+Open data
-Basic information
Entry | Database: PDB / ID: 3bnw | ||||||
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Title | Crystal structure of riboflavin kinase from Trypanosoma brucei | ||||||
Components | Riboflavin kinase, putative | ||||||
Keywords | TRANSFERASE / apo structure / Structural Genomics / Structural Genomics of Pathogenic Protozoa Consortium / SGPP / Kinase / PSI-2 / Protein Structure Initiative | ||||||
Function / homology | Function and homology information riboflavin metabolic process / riboflavin kinase / riboflavin kinase activity / FMN biosynthetic process / response to xenobiotic stimulus => GO:0009410 / riboflavin biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Merritt, E.A. / Holmes, M. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP) | ||||||
Citation | Journal: To be Published Title: Riboflavin kinase from Trypanosoma brucei. Authors: Merritt, E.A. / Holmes, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bnw.cif.gz | 74.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bnw.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bnw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/3bnw ftp://data.pdbj.org/pub/pdb/validation_reports/bn/3bnw | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 20624.361 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb09.211.3420 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PlysS / References: UniProt: Q38DG4, riboflavin kinase #2: 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: 1.92 Å3/Da / Density % sol: 36.08 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 20% PEG 3350, 0.28M KF, 0.1M HEPES, 5mM DTT, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97915 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 22, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→38.6 Å / Num. all: 10719 / Num. obs: 10719 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 10.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Hybrid model generated by Rosetta Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.89 / SU B: 29.819 / SU ML: 0.326 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 6.294 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FROM TLS REFINEMENT, ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.677 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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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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