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Yorodumi- PDB-2vbt: Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vbt | ||||||
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Title | Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP and PO4 | ||||||
Components | RIBOFLAVIN KINASE | ||||||
Keywords | TRANSFERASE / CRADLE-LOOP BARREL / CTP-DEPENDENT KINASE / FMN | ||||||
Function / homology | Function and homology information CTP-dependent riboflavin kinase / riboflavin kinase activity / FMN biosynthetic process / riboflavin biosynthetic process / phosphorylation / nucleotide binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | METHANOCOCCUS JANNASCHII (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Hartmann, M.D. / Ammelburg, M. / Djuranovic, S. / Martin, J. / Lupas, A.N. / Zeth, K. | ||||||
Citation | Journal: Structure / Year: 2007 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vbt.cif.gz | 43.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vbt.ent.gz | 29.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vbt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/2vbt ftp://data.pdbj.org/pub/pdb/validation_reports/vb/2vbt | HTTPS FTP |
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-Related structure data
Related structure data | 2p3mC 2vbsSC 2vbuC 2vbvC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) METHANOCOCCUS JANNASCHII (archaea) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q60365, CTP-dependent riboflavin kinase |
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#2: Chemical | ChemComp-CDP / |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: 40% V/V ETHYLENE GLYCOL, 100 MM PHOSPHATE-CITRATE PH 4.2, 200 MM NH4SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9762 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→38.32 Å / Num. obs: 9448 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.57 |
Reflection shell | Resolution: 2.7→2.87 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.02 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VBS Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.263 / 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: 60.53 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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