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- PDB-2vbs: Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vbs | ||||||
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Title | Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with PO4 | ||||||
![]() | RIBOFLAVIN KINASE![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hartmann, M.D. / Djuranovic, S. / Ammelburg, M. / 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 DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40.4 KB | Display | ![]() |
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PDB format | ![]() | 27.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2p3mSC ![]() 2vbtC ![]() 2vbuC ![]() 2vbvC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 15709.521 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q60365, ![]() | ||
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#2: Chemical | ChemComp-PO4 / ![]() | ||
#3: Chemical | ChemComp-ZN / | ||
#4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.3 Å3/Da / Density % sol: 76.7 % / Description: NONE |
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Crystal grow![]() | Details: 2M NH4SO4 |
-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![]() |
Reflection | Resolution: 3→19.99 Å / Num. obs: 6951 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.28 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.43 |
Reflection shell | Resolution: 3→3.2 Å / Redundancy: 4.43 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.39 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2P3M Resolution: 3→19.99 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.868 / Cross valid method: THROUGHOUT / ESU R: 0.476 / ESU R Free: 0.347 / 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: 49.89 Å2
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Refinement step | Cycle: LAST / Resolution: 3→19.99 Å
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Refine LS restraints |
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