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Yorodumi- PDB-3fyn: Crystal structure from the mobile metagenome of Cole Harbour Salt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fyn | ||||||
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Title | Crystal structure from the mobile metagenome of Cole Harbour Salt Marsh: Integron Cassette Protein HFX_CASS3 | ||||||
Components | Integron gene cassette protein HFX_CASS3 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Integron Cassette Protein / Mobile Metagenome / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.449 Å | ||||||
Authors | Sureshan, V. / Deshpande, C.N. / Harrop, S.J. / Kudritska, M. / Koenig, J.E. / Evdokimova, E. / Osipiuk, J. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. ...Sureshan, V. / Deshpande, C.N. / Harrop, S.J. / Kudritska, M. / Koenig, J.E. / Evdokimova, E. / Osipiuk, J. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Doolittle, W.F. / Stokes, H.W. / Curmi, P.M.G. / Mabbutt, B.C. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Structure from the mobile metagenome of Cole Harbour Salt Marsh: Integron Cassette Protein HFX_CASS3 Authors: Sureshan, V. / Deshpande, C. / Harrop, S.J. / Kudritska, M. / Koenig, J.E. / Evdokimova, E. / Osipiuk, J. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Doolittle, W.F. / Stokes, H.W. / ...Authors: Sureshan, V. / Deshpande, C. / Harrop, S.J. / Kudritska, M. / Koenig, J.E. / Evdokimova, E. / Osipiuk, J. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Doolittle, W.F. / Stokes, H.W. / Curmi, P.M.G. / Mabbutt, B.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fyn.cif.gz | 74.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fyn.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 3fyn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fyn_validation.pdf.gz | 435.1 KB | Display | wwPDB validaton report |
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Full document | 3fyn_full_validation.pdf.gz | 436.3 KB | Display | |
Data in XML | 3fyn_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 3fyn_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/3fyn ftp://data.pdbj.org/pub/pdb/validation_reports/fy/3fyn | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19244.275 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: ORF1 / Plasmid: p15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: B0BFQ1 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ACT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 29.6 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 0.2 M Magnesium acetate, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97923 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Oct 13, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 1.449→50 Å / Num. all: 23542 / Num. obs: 23542 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 16.14 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Χ2: 1.707 / Net I/σ(I): 24.992 |
Reflection shell | Resolution: 1.449→1.53 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 1.906 / Num. unique all: 1075 / Rsym value: 0.696 / Χ2: 0.84 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.449→27.985 Å / Occupancy max: 1 / Occupancy min: 0.16 / SU ML: 0.19 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.816 Å2 / ksol: 0.407 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.61 Å2 / Biso mean: 22.616 Å2 / Biso min: 8.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.449→27.985 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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