+Open data
-Basic information
Entry | Database: PDB / ID: 1nb0 | ||||||
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Title | Crystal Structure of Human Riboflavin Kinase | ||||||
Components | hypothetical protein FLJ11149Hypothesis | ||||||
Keywords | TRANSFERASE / BETA BARREL | ||||||
Function / homology | Function and homology information flavin adenine dinucleotide biosynthetic process / Vitamin B2 (riboflavin) metabolism / riboflavin metabolic process / riboflavin kinase / riboflavin kinase activity / FMN biosynthetic process / positive regulation of NAD(P)H oxidase activity / riboflavin biosynthetic process / reactive oxygen species metabolic process / phosphorylation ...flavin adenine dinucleotide biosynthetic process / Vitamin B2 (riboflavin) metabolism / riboflavin metabolic process / riboflavin kinase / riboflavin kinase activity / FMN biosynthetic process / positive regulation of NAD(P)H oxidase activity / riboflavin biosynthetic process / reactive oxygen species metabolic process / phosphorylation / apoptotic process / mitochondrion / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Karthikeyan, S. / Zhou, Q. / Mseeh, F. / Grishin, N.V. / Osterman, A.L. / Zhang, H. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Crystal Structure of Human Riboflavin Kinase Reveals a Beta Barrel Fold and a Novel Active Site Arch Authors: Karthikeyan, S. / Zhou, Q. / Mseeh, F. / Grishin, N.V. / Osterman, A.L. / Zhang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nb0.cif.gz | 47.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nb0.ent.gz | 32.7 KB | Display | PDB format |
PDBx/mmJSON format | 1nb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/1nb0 ftp://data.pdbj.org/pub/pdb/validation_reports/nb/1nb0 | HTTPS FTP |
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-Related 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: 16772.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FLJ11149 / Organ: brain / Plasmid: pPROEX-Hta / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q969G6, riboflavin kinase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ADP / |
#4: 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: 2.06 Å3/Da / Density % sol: 39.69 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: NA cadodalyte, Mg acetate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / PH range low: 7.4 / PH range high: 7.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.008 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Aug 25, 2002 / Details: MIRROR |
Radiation | Monochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 17010 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 12.47 % / Biso Wilson estimate: 20.32 Å2 / Rsym value: 0.036 / Net I/σ(I): 49.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Mean I/σ(I) obs: 4.3 / Rsym value: 0.2 / % possible all: 83.2 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 50 Å / Num. obs: 16996 / Num. measured all: 212199 / Rmerge(I) obs: 0.036 |
Reflection shell | *PLUS % possible obs: 83.2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→49.39 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.264 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.113 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→49.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.698→1.742 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Origin x: 23.986 Å / Origin y: 6.416 Å / Origin z: 7.882 Å
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.187 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.74 Å |