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Yorodumi- PDB-4cfs: CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUIN... -
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-Basic information
Entry | Database: PDB / ID: 4cfs | ||||||
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Title | CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) CATALYTICALLY INACTIVE H251A VARIANT COMPLEXED WITH ITS NATURAL SUBSTRATE 1-H-3-HYDROXY-4- OXOQUINALDINE | ||||||
Components | 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / ALPHA-BETA HYDROLASE COMPLEX / DIOXYGENASE / COFACTOR-DEVOID | ||||||
Function / homology | Function and homology information 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase / 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / : Similarity search - Function | ||||||
Biological species | ARTHROBACTER NITROGUAJACOLICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.94 Å | ||||||
Authors | Bui, S. / Steiner, R.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Origin of the Proton-Transfer Step in the Cofactor-Free 1-H-3-Hydroxy-4-Oxoquinaldine 2,4- Dioxygenase: Effect of the Basicity of an Active Site His Residue. Authors: Hernandez-Ortega, A. / Quesne, M.G. / Bui, S. / Heuts, D.P. / Steiner, R.A. / Heyes, D.J. / De Visser, S.P. / Scrutton, N.S. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structural Basis for Cofactor-Independent Dioxygenation of N-Heteroaromatic Compounds at the Alpha/Beta-Hydrolase Fold. Authors: Steiner, R.A. / Janssen, H.J. / Roversi, P. / Oakley, A.J. / Fetzner, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cfs.cif.gz | 244.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cfs.ent.gz | 204.9 KB | Display | PDB format |
PDBx/mmJSON format | 4cfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cfs_validation.pdf.gz | 491.1 KB | Display | wwPDB validaton report |
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Full document | 4cfs_full_validation.pdf.gz | 504.3 KB | Display | |
Data in XML | 4cfs_validation.xml.gz | 49 KB | Display | |
Data in CIF | 4cfs_validation.cif.gz | 68.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/4cfs ftp://data.pdbj.org/pub/pdb/validation_reports/cf/4cfs | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 33107.195 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARTHROBACTER NITROGUAJACOLICUS (bacteria) Strain: RU61A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15/PREP4 References: UniProt: O31266, 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-HQD / #4: Chemical | ChemComp-TAR / #5: Water | ChemComp-HOH / | Sequence details | MRGSHHHHHH | |
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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: 2.56 Å3/Da / Density % sol: 51.96 % / Description: NONE |
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Crystal grow | pH: 7 Details: PROTEIN AT 150 MG/ML IN STORAGE BUFFER 1.65M NA/K TARTRATE, 0.1M HEPES PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 | |||||||||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 5, 2010 / Details: MIRRORS | |||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.95→46.45 Å / Num. obs: 92811 / % possible obs: 100 % / Observed criterion σ(I): -1 / Redundancy: 7.73 % / Biso Wilson estimate: 24.648 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.5 | |||||||||||||||
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 7.84 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.94→46.45 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.588 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TNCS IS PRESENT FRAC 0.000 0.407 0.407
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.945 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→46.45 Å
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Refine LS restraints |
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