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Open data
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Basic information
Entry | Database: PDB / ID: 5fo0 | ||||||
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Title | D298E mutant of FAD synthetase from Corynebacterium ammoniagenes | ||||||
![]() | RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF | ||||||
![]() | TRANSFERASE / RIBOFLAVIN KINASE / NUCLEOTIDE-BINDING / ATP- BINDING / MULTIFUNCTIONAL ENZYME / NUCLEOTIDYLTRANSFERASE | ||||||
Function / homology | ![]() riboflavin kinase / FAD synthase / FMN adenylyltransferase activity / FAD biosynthetic process / riboflavin kinase activity / FMN biosynthetic process / riboflavin biosynthetic process / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Martinez-Julvez, M. / Herguedas, B. / Milagros, M. | ||||||
![]() | ![]() Title: The trimer interface in the quaternary structure of the bifunctional prokaryotic FAD synthetase from Corynebacterium ammoniagenes. Authors: Serrano, A. / Sebastian, M. / Arilla-Luna, S. / Baquedano, S. / Herguedas, B. / Velazquez-Campoy, A. / Martinez-Julvez, M. / Medina, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.1 KB | Display | ![]() |
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PDB format | ![]() | 111.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.8 KB | Display | ![]() |
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Full document | ![]() | 460.3 KB | Display | |
Data in XML | ![]() | 25.7 KB | Display | |
Data in CIF | ![]() | 35.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fnzC ![]() 5fo1C ![]() 2x0kS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 1 - 338 / Label seq-ID: 1 - 338
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Components
#1: Protein | Mass: 36896.387 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q59263, riboflavin kinase, FAD synthase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | MUTATION D298E | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.71 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: PROTEIN WAS CRYSTALLIZED FROM 1.5 M LI2SO4, 100 MM HEPES, PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 11, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→47.09 Å / Num. obs: 26982 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 2.51→2.65 Å / Redundancy: 7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.6 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2X0K Resolution: 2.51→45 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.894 / SU B: 9.762 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.575 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 259-262 OF CHAINS A AND B COULD NOT BE REFINED BECAUSE OF THE LACK OF ELECTRON DENSITY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.842 Å2
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Refinement step | Cycle: LAST / Resolution: 2.51→45 Å
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Refine LS restraints |
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