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- PDB-2vbv: Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vbv | ||||||
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Title | Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP and FMN | ||||||
![]() | RIBOFLAVIN KINASE | ||||||
![]() | TRANSFERASE / CRADLE-LOOP BARREL / CTP-DEPENDENT KINASE / FMN | ||||||
Function / homology | ![]() CTP-dependent riboflavin kinase / riboflavin kinase activity / FMN biosynthetic process / riboflavin biosynthetic process / phosphorylation / nucleotide binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hartmann, M.D. / Ammelburg, M. / Djuranovic, S. / Martin, J. / Lupas, A.N. / Zeth, K. | ||||||
![]() | ![]() Title: A Ctp-Dependent Archaeal Riboflavin Kinase Forms a Bridge in the Evolution of Cradle-Loop Barrels. Authors: Ammelburg, M. / Hartmann, M.D. / Djuranovic, S. / Alva, V. / Koretke, K.K. / Martin, J. / Sauer, G. / Truffault, V. / Zeth, K. / Lupas, A.N. / Coles, M. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.9 KB | Display | ![]() |
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PDB format | ![]() | 53.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 19.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2p3mC ![]() 2vbsC ![]() 2vbtSC ![]() 2vbuC 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: 15709.521 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q60365, CTP-dependent riboflavin kinase |
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-Non-polymers , 6 types, 80 molecules ![](data/chem/img/CDP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-IOD / | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-FMN / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.8 % / Description: NONE |
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Crystal grow | Details: 20% W/V PEG 8000, 200 MM SODIUM IODIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2141 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→38.58 Å / Num. obs: 12903 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.67 |
Reflection shell | Resolution: 2.4→2.55 Å / Redundancy: 5.62 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.25 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VBT Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.876 / Cross valid method: THROUGHOUT / ESU R: 0.501 / ESU R Free: 0.345 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.39 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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