+Open data
-Basic information
Entry | Database: PDB / ID: 5xv0 | ||||||
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Title | Crystal structure of Rib7 mutant D33N from Methanosarcina mazei | ||||||
Components | Conserved protein | ||||||
Keywords | OXIDOREDUCTASE / Rib7 / riboflavin biosynthesis | ||||||
Function / homology | Function and homology information 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase / 5-amino-6-(5-phosphoribosylamino)uracil reductase activity / riboflavin biosynthetic process / NADP binding Similarity search - Function | ||||||
Biological species | Methanosarcina mazei (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Yeh, T.M. / Chen, S.C. / Chang, T.H. / Huang, M.F. / Liaw, S.H. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2018 Title: Evolution of archaeal Rib7 and eubacterial RibG reductases in riboflavin biosynthesis: Substrate specificity and cofactor preference. Authors: Chen, S.C. / Yen, T.M. / Chang, T.H. / Liaw, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xv0.cif.gz | 288.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xv0.ent.gz | 234.8 KB | Display | PDB format |
PDBx/mmJSON format | 5xv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xv0_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 5xv0_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 5xv0_validation.xml.gz | 59.2 KB | Display | |
Data in CIF | 5xv0_validation.cif.gz | 81.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/5xv0 ftp://data.pdbj.org/pub/pdb/validation_reports/xv/5xv0 | HTTPS FTP |
-Related structure data
Related structure data | 5xuxSC 5xv2C 5xv5C 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26104.125 Da / Num. of mol.: 6 / Mutation: D33N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88) (archaea) Strain: ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88 Gene: MM_0826 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PYN5 #2: Chemical | ChemComp-NAP / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10 % Tacsimate (pH 7.0), 10 % PEG 5000, and 100 mM HEPES (pH 7.0) |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. obs: 141352 / % possible obs: 99.9 % / Redundancy: 5.8 % / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.652 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XUX Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.908 / SU B: 4.783 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.167 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.209 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→30 Å
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Refine LS restraints |
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