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Yorodumi- PDB-7ojm: CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ojm | ||||||
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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 2-METHYL-QUINOLIN-4(1H)-ONE UNDER NORMOXIC CONDITIONS | ||||||
Components | 1H-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 | Paenarthrobacter nitroguajacolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å | ||||||
Authors | Bui, S. / Steiner, R.A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Chem Sci / Year: 2023 Title: Evolutionary adaptation from hydrolytic to oxygenolytic catalysis at the alpha / beta-hydrolase fold. Authors: Bui, S. / Gil-Guerrero, S. / van der Linden, P. / Carpentier, P. / Ceccarelli, M. / Jambrina, P.G. / Steiner, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ojm.cif.gz | 140.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ojm.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ojm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/7ojm ftp://data.pdbj.org/pub/pdb/validation_reports/oj/7ojm | HTTPS FTP |
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-Related structure data
Related structure data | 7okzC 8a97C 8oroC 8oxnC 8oxtC 4cfsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 3 - 275 / Label seq-ID: 15 - 287
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
-Protein , 1 types, 2 molecules AAABBB
#1: Protein | Mass: 33222.324 Da / Num. of mol.: 2 / Mutation: C69S, H251A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenarthrobacter nitroguajacolicus (bacteria) Gene: hod, meqE, ARUE_113p00080, pAL1.008 / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15/PREP4 References: UniProt: O31266, 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase |
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-Non-polymers , 6 types, 257 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SRT / #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.38 Å3/Da / Density % sol: 48.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / 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 / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2015 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.91741 Å / Relative weight: 1 | ||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2→44.44 Å / Num. obs: 42360 / % possible obs: 99.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.05 / Net I/σ(I): 10.5 | ||||||||||||||||||
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2876 / Rpim(I) all: 0.407 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CFS Resolution: 2.001→42.14 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.297 / SU ML: 0.127 / Cross valid method: FREE R-VALUE / ESU R: 0.043 / ESU R Free: 0.036 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.536 Å2
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Refinement step | Cycle: LAST / Resolution: 2.001→42.14 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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