+Open data
-Basic information
Entry | Database: PDB / ID: 1nb9 | ||||||
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Title | Crystal Structure of Riboflavin Kinase | ||||||
Components | hypothetical protein FLJ11149Hypothesis | ||||||
Keywords | TRANSFERASE / BETA BARREL / RIBOFLAVIN / RIBOFLAVIN KINASE | ||||||
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 / MOLECULAR REPLACEMENT / 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 | 1nb9.cif.gz | 50 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nb9.ent.gz | 33.4 KB | Display | PDB format |
PDBx/mmJSON format | 1nb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/1nb9 ftp://data.pdbj.org/pub/pdb/validation_reports/nb/1nb9 | HTTPS FTP |
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-Related structure data
Related structure data | 1nb0SC 1p4mC S: Starting model for refinement C: citing same article (ref.) |
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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: 16772.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FLJ11149 / 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: Chemical | ChemComp-RBF / |
#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: 2.01 Å3/Da / Density % sol: 38.18 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 5, 2002 / Details: OSMIC MIRROR |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 17163 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 26.838 Å2 / Rsym value: 0.03 / Net I/σ(I): 42.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 1557 / Rsym value: 0.263 / % possible all: 90.3 |
Reflection | *PLUS Num. obs: 17151 / Num. measured all: 251797 / Rmerge(I) obs: 0.03 |
Reflection shell | *PLUS % possible obs: 90.3 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 3.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NB0 Resolution: 1.7→49.39 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.024 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.104 / 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: 20.827 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: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -6.314 Å / Origin y: 23.839 Å / Origin z: 33.411 Å
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.206 / Rfactor Rwork: 0.184 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |