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Yorodumi- PDB-5epd: Crystal structure of Glycerol Trinitrate Reductase XdpB from Agro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5epd | ||||||
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Title | Crystal structure of Glycerol Trinitrate Reductase XdpB from Agrobacterium sp. R89-1 (Apo form) | ||||||
Components | Glycerol trinitrate reductase | ||||||
Keywords | OXIDORECCTASE / Old Yellow Enzyme family TIM barrel fold GTN Reductase Xenobiotic degradation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Kolenko, P. / Zahradnik, J. / Zuskova, I. / Cerny, J. / Palyzova, A. / Kyslikova, E. / Schneider, B. | ||||||
Funding support | Czech Republic, 1items
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Citation | Journal: PLoS ONE / Year: 2018 Title: The crystal structure of XdpB, the bacterial old yellow enzyme, in an FMN-free form. Authors: Zahradnik, J. / Kolenko, P. / Palyzova, A. / Cerny, J. / Kolarova, L. / Kyslikova, E. / Maresova, H. / Grulich, M. / Nunvar, J. / Sulc, M. / Kyslik, P. / Schneider, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5epd.cif.gz | 82 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5epd.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 5epd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/5epd ftp://data.pdbj.org/pub/pdb/validation_reports/ep/5epd | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 41141.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: C-terminal pentapeptide region tightly interact with the crystal symmetry mate. FMN site is not occupied. Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: xdpB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ArcticExpress / References: UniProt: A0A0A0VDJ9 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.61 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8.02 Details: 50 mM tri-Lithium citrate, 32 % (w/v) PEG 3350, not buffered |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.36 Å / Num. all: 21254 / Num. obs: 20170 / % possible obs: 94 % / Redundancy: 3.7 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.1 / % possible all: 86.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→47.36 Å / Cor.coef. Fo:Fc: 0.951 / SU B: 5.784 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.246 / 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: 37 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→47.36 Å
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Refine LS restraints |
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