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- PDB-5a8a: Crystal structure of the riboflavin kinase module of FAD syntheta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a8a | ||||||
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Title | Crystal structure of the riboflavin kinase module of FAD synthetase from Corynebacterium ammoniagenes in complex with FMN and ADP (P3 2 21) | ||||||
![]() | RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF | ||||||
![]() | TRANSFERASE / RIBOFLAVIN KINASE DOMAIN / ATP-BINDING / NUCLEOTIDE-BINDING | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Herguedas, B. / Martinez-Julvez, M. / Hermoso, J.A. / Medina, M. | ||||||
![]() | ![]() Title: Structural Insights Into the Synthesis of Fmn in Prokaryotic Organisms. Authors: Herguedas, B. / Lans, I. / Sebastian, M. / Hermoso, J.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 | ![]() | 116 KB | Display | ![]() |
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PDB format | ![]() | 89.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 25.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a88C ![]() 5a89C ![]() 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 17135.146 Da / Num. of mol.: 2 / Fragment: RIBOFLAVIN KINASE DOMAIN, RESIDUES 183-338 Source method: isolated from a genetically manipulated source Details: KINASE DOMAIN OF FAD SYNTHETASE (A BIFUNCTIONAL ENZYME) Source: (gene. exp.) ![]() Plasmid: PET28A / Production host: ![]() ![]() |
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-Non-polymers , 7 types, 332 molecules ![](data/chem/img/FMN.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | TRUNCATED SEQUENCE OF CAFADS (FROM 183 TO 338 RESIDUE). |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64 % Description: ONLY RFK MODULE OF CAFDS-2X0K-AS SEARCHING MODEL |
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Crystal grow | pH: 5 Details: 26-30% PEG 4000, 200 MM LI2SO4 AND 100 MM SODIUM ACETATE PH 5.0 AND 100 MM NAI |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→36.79 Å / Num. obs: 43268 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4 / % possible all: 89.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2X0K Resolution: 1.8→63.81 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.525 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FINAL MODEL INCLUDES RESIDUES 184-337 IN CHAIN A AND 185- -338 IN CHAIN B
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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: 20.913 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→63.81 Å
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Refine LS restraints |
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