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Yorodumi- PDB-6ypv: Alpha-ketoglutarate-dependent dioxygenase AlkB in complex with Fe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ypv | ||||||||||||
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Title | Alpha-ketoglutarate-dependent dioxygenase AlkB in complex with Fe and AKG after oxygen exposure using FT-SSX methods | ||||||||||||
Components | Alpha-ketoglutarate-dependent dioxygenase AlkB | ||||||||||||
Keywords | OXIDOREDUCTASE / iron dependent dioxygenase / DNA repait / 2-oxoglutarate | ||||||||||||
Function / homology | Function and homology information response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / : / : / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / DNA alkylation repair ...response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / : / : / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / DNA alkylation repair / oxidative demethylation / DNA demethylation / dioxygenase activity / ferrous iron binding / DNA repair / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||||||||
Authors | Rabe, P. / Beale, J.H. / Lang, P.A. / Dirr, A.S. / Leissing, T.M. / Butryn, A. / Aller, P. / Kamps, J.J.A.G. / Axford, D. / McDonough, M.A. ...Rabe, P. / Beale, J.H. / Lang, P.A. / Dirr, A.S. / Leissing, T.M. / Butryn, A. / Aller, P. / Kamps, J.J.A.G. / Axford, D. / McDonough, M.A. / Orville, A.M. / Owen, R. / Schofield, C.J. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Iucrj / Year: 2020 Title: Anaerobic fixed-target serial crystallography. Authors: Rabe, P. / Beale, J.H. / Butryn, A. / Aller, P. / Dirr, A. / Lang, P.A. / Axford, D.N. / Carr, S.B. / Leissing, T.M. / McDonough, M.A. / Davy, B. / Ebrahim, A. / Orlans, J. / Storm, S.L.S. / ...Authors: Rabe, P. / Beale, J.H. / Butryn, A. / Aller, P. / Dirr, A. / Lang, P.A. / Axford, D.N. / Carr, S.B. / Leissing, T.M. / McDonough, M.A. / Davy, B. / Ebrahim, A. / Orlans, J. / Storm, S.L.S. / Orville, A.M. / Schofield, C.J. / Owen, R.L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ypv.cif.gz | 147.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ypv.ent.gz | 95.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ypv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/6ypv ftp://data.pdbj.org/pub/pdb/validation_reports/yp/6ypv | HTTPS FTP |
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-Related structure data
Related structure data | 6y0nC 6y0oC 6y0qC 6y12C 4jhtS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24103.502 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Gene: alkB, aidD, b2212, JW2200 / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05050, DNA oxidative demethylase |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-AKG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.29 % |
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Crystal grow | Temperature: 298 K / Method: batch mode Details: 25% w/v PEG 3350, 5% v/v glycerol and 200 mM sodium ormate |
-Data collection
Diffraction | Mean temperature: 293 K / Ambient temp details: room temperature / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2019 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96863 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→39.35 Å / Num. obs: 11994 / % possible obs: 100 % / Redundancy: 25.8 % / Biso Wilson estimate: 23.04 Å2 / CC1/2: 0.874 / R split: 0.333 / Net I/σ(I): 48.4 |
Reflection shell | Resolution: 2.1→2.136 Å / Mean I/σ(I) obs: 8.795 / Num. unique obs: 593 / CC1/2: 0.414 / R split: 0.617 |
Serial crystallography measurement | Collimation: KB mirrors / Source size: 49 µm2 |
Serial crystallography sample delivery | Description: fixed target / Method: fixed target |
Serial crystallography sample delivery fixed target | Description: FixedTarget Chip |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JHT Resolution: 2.1→39.35 Å / SU ML: 0.2596 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.3511
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→39.35 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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