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Yorodumi- PDB-1x6m: Crystal structure of the glutathione-dependent formaldehyde-activ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x6m | ||||||
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Title | Crystal structure of the glutathione-dependent formaldehyde-activating enzyme (Gfa) | ||||||
Components | Glutathione-dependent formaldehyde-activating enzyme | ||||||
Keywords | LYASE / zn-enzyme / formaldehyde / 3_10 helix | ||||||
Function / homology | Function and homology information S-(hydroxymethyl)glutathione synthase / S-(hydroxymethyl)glutathione synthase activity / formaldehyde catabolic process / zinc ion binding Similarity search - Function | ||||||
Biological species | Paracoccus denitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Se-SAD / Resolution: 2.35 Å | ||||||
Authors | Neculai, A.M. / Neculai, D. / Vorholt, J.A. / Becker, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: A dynamic zinc redox switch Authors: Neculai, A.M. / Neculai, D. / Griesinger, C. / Vorholt, J.A. / Becker, S. #1: Journal: J.Biol.Chem. / Year: 2002 Title: A glutathione-dependent formaldehyde-activating enzyme (Gfa) from Paracoccus denitrificans detected and purified via two-dimensional proton exchange NMR spectroscopy Authors: Goenrich, M. / Bartoschek, S. / Hagemeier, C.H. / Griesinger, C. / Vorholt, J.A. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x6m.cif.gz | 165.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x6m.ent.gz | 132.6 KB | Display | PDB format |
PDBx/mmJSON format | 1x6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x6m_validation.pdf.gz | 486.4 KB | Display | wwPDB validaton report |
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Full document | 1x6m_full_validation.pdf.gz | 507.1 KB | Display | |
Data in XML | 1x6m_validation.xml.gz | 34.5 KB | Display | |
Data in CIF | 1x6m_validation.cif.gz | 48.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/1x6m ftp://data.pdbj.org/pub/pdb/validation_reports/x6/1x6m | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a dimer |
-Components
#1: Protein | Mass: 21191.076 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Gene: gfa / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q51669, Lyases; Carbon-sulfur lyases #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #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: 3.6 Å3/Da / Density % sol: 65.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: (NH4)2SO4, PEG 400, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9798 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 18, 2004 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→74.33 Å / Num. all: 49354 / Num. obs: 49354 / % possible obs: 99.8 % / Observed criterion σ(F): 2.08 / Observed criterion σ(I): 2.08 / Redundancy: 1.95 % / Rmerge(I) obs: 0.077 / Rsym value: 0.0889 / Net I/σ(I): 8.66 |
Reflection shell | Resolution: 2.35→2.45 Å / Redundancy: 1.96 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2.17 / Num. unique all: 5774 / Rsym value: 0.4846 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: Se-SAD / Resolution: 2.35→74.29 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.907 / SU B: 6.78 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 2.08 / ESU R: 0.25 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 38.04 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→74.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 Å / Total num. of bins used: 20
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