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Yorodumi- PDB-6npa: X-ray crystal structure of TmpB, (R)-1-hydroxy-2-trimethylaminoet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6npa | ||||||
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Title | X-ray crystal structure of TmpB, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase, with (R)-1-hydroxy-2-trimethylaminoethylphosphonate | ||||||
Components | TmpB, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase | ||||||
Keywords | OXIDOREDUCTASE / organophosphonate / iron oxygenase / HD-domain / gene annotation / enzyme | ||||||
Function / homology | Function and homology information [1-hydroxy-2-(trimethylamino)ethyl]phosphonate dioxygenase (glycine-betaine-forming) / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Leisingera caerulea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Rajakovich, L.J. / Mitchell, A.J. / Boal, A.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2019 Title: A New Microbial Pathway for Organophosphonate Degradation Catalyzed by Two Previously Misannotated Non-Heme-Iron Oxygenases. Authors: Rajakovich, L.J. / Pandelia, M.E. / Mitchell, A.J. / Chang, W.C. / Zhang, B. / Boal, A.K. / Krebs, C. / Bollinger Jr., J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6npa.cif.gz | 165.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6npa.ent.gz | 128.9 KB | Display | PDB format |
PDBx/mmJSON format | 6npa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6npa_validation.pdf.gz | 5.9 MB | Display | wwPDB validaton report |
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Full document | 6npa_full_validation.pdf.gz | 5.9 MB | Display | |
Data in XML | 6npa_validation.xml.gz | 29.6 KB | Display | |
Data in CIF | 6npa_validation.cif.gz | 41.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/6npa ftp://data.pdbj.org/pub/pdb/validation_reports/np/6npa | HTTPS FTP |
-Related structure data
Related structure data | 6npbC 6npcC 6npdC 4mlmS 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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Unit cell |
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-Components
#1: Protein | Mass: 23057.904 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leisingera caerulea (bacteria) / Plasmid: pET-28a(+) / Details (production host): NdeI/XhoI / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4V8H040*PLUS, Oxidoreductases #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-FE2 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.1 Å3/Da / Density % sol: 37.02 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10 mg/mL TmpB, 0.2 M calcium chloride, 0.1 M HEPES, pH 7.5, 27-33% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 6, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.73→50 Å / Num. obs: 76571 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.026 / Rrim(I) all: 0.072 / Χ2: 0.902 / Net I/σ(I): 7.6 / Num. measured all: 568175 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4MLM Resolution: 1.73→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.853 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.129 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.85 Å2 / Biso mean: 23.865 Å2 / Biso min: 8.01 Å2
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Refinement step | Cycle: final / Resolution: 1.73→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.718→1.763 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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