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Yorodumi- PDB-2wj6: CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wj6 | ||||||
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Title | CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) FROM ARTHROBACTER NITROGUAJACOLICUS RU61A COMPLEXED WITH ITS NATURAL PRODUCT N- ACETYLANTHRANILATE | ||||||
Components | 1H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / ALPHA/BETA HYDROLASE | ||||||
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: 2 Å | ||||||
Authors | Steiner, R.A. | ||||||
Citation | 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. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Crystallization and Preliminary X-Ray Analysis of 1H-3-Hydroxy-4-Oxoquinaldine 2,4-Dioxygenase from Arthrobacter Nitroguajacolicus Ru61A: A Cofactor-Devoid Dioxygenase of the Alpha/Beta-Hydrolase-Fold Superfamily. Authors: Steiner, R.A. / Frerichs-Deeken, U. / Fetzner, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wj6.cif.gz | 247.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wj6.ent.gz | 207.9 KB | Display | PDB format |
PDBx/mmJSON format | 2wj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wj6_validation.pdf.gz | 502.9 KB | Display | wwPDB validaton report |
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Full document | 2wj6_full_validation.pdf.gz | 534.1 KB | Display | |
Data in XML | 2wj6_validation.xml.gz | 54.1 KB | Display | |
Data in CIF | 2wj6_validation.cif.gz | 73.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/2wj6 ftp://data.pdbj.org/pub/pdb/validation_reports/wj/2wj6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 31883.863 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: A4V8M9, UniProt: O31266*PLUS, 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase |
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-Non-polymers , 5 types, 772 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-ZZ8 / #5: Chemical | ChemComp-SRT / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 69 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 69 TO SER ...ENGINEERED |
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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: 2.27 Å3/Da / Density % sol: 45.29 % / 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: 0.9796 | |||||||||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 6, 2008 / Details: MIRRORS | |||||||||||||||
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2→30 Å / Num. obs: 86312 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 22.46 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19 | |||||||||||||||
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.7 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: OTHER / Resolution: 2→38.52 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.846 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.032 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.821 Å2
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Refinement step | Cycle: LAST / Resolution: 2→38.52 Å
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Refine LS restraints |
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