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- PDB-2wj3: CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUIN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wj3 | ||||||
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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 | ||||||
![]() | 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE | ||||||
![]() | OXIDOREDUCTASE / ALPHA/BETA HYDROLASE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Steiner, R.A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 233.5 KB | Display | ![]() |
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PDB format | ![]() | 190.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.2 KB | Display | ![]() |
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Full document | ![]() | 494 KB | Display | |
Data in XML | ![]() | 45.3 KB | Display | |
Data in CIF | ![]() | 61 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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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: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 3 / Auth seq-ID: 5 - 274 / Label seq-ID: 5 - 274
NCS oper:
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Components
#1: Protein | Mass: 31883.863 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: RU61A / Production host: ![]() ![]() References: UniProt: A4V8M9, UniProt: O31266*PLUS, 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase #2: Chemical | #3: Chemical | ChemComp-SRT / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 69 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 69 TO SER ...ENGINEERED | Nonpolymer details | GLYCEROL (GOL): PRESENT IN THE SOLUTION FOR CRYOPROTECTION D(-)-TARTARIC ACID (TAR): PRESENT IN THE ...GLYCEROL (GOL): PRESENT IN THE SOLUTION FOR CRYOPROTEC | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.21 % / Description: NONE |
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Crystal grow | pH: 7 Details: HIS6-HOD AT 150 MG/ML IN STORAGE BUFFER IN THE PRESENCE OF A RESERVOIR COMPOSED OF 1.65 M SODIUM/POTASSIUM TARTRATE, 0.1 M HEPES PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 23, 2009 / Details: MIRRORS | |||||||||||||||
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9745 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.09→53.15 Å / Num. obs: 75553 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.8 | |||||||||||||||
Reflection shell | Resolution: 2.09→2.21 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 5.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: HOD H251A MUTANT SOLVED BY SAD IN SPACE GROUP P 43 21 2 AND NOT FULLY REFINED Resolution: 2.09→53.16 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.948 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 32.15 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→53.16 Å
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Refine LS restraints |
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