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Yorodumi- PDB-3fuy: Structure from the mobile metagenome of Cole Harbour Salt Marsh: ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fuy | ||||||
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Title | Structure from the mobile metagenome of Cole Harbour Salt Marsh: Integron Cassette Protein HFX_CASS1 | ||||||
Components | Putative integron gene cassette protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Integron cassette protein / Mobile Metagenome / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Structure from the mobile metagenome of cole harbour salt marsh: integron cassette protein hfx_cass1 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Putative integron gene cassette protein Function and homology information | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Sureshan, V. / Deshpande, C.N. / Harrop, S.J. / Kudrytska, M. / Koenig, J.E. / Evdokimova, E. / Osipiuk, J. / Edwards, A. / Savchenko, A. / Joachimiak, A. ...Sureshan, V. / Deshpande, C.N. / Harrop, S.J. / Kudrytska, M. / Koenig, J.E. / Evdokimova, E. / Osipiuk, J. / Edwards, A. / 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: Plos One / Year: 2013 Title: Integron gene cassettes: a repository of novel protein folds with distinct interaction sites Authors: Sureshan, V. / Deshpande, C.N. / Boucher, Y. / Koenig, J.E. / Stokes, H.W. / Harrop, S.J. / 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 | 3fuy.cif.gz | 103.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fuy.ent.gz | 84.6 KB | Display | PDB format |
PDBx/mmJSON format | 3fuy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/3fuy ftp://data.pdbj.org/pub/pdb/validation_reports/fu/3fuy | HTTPS FTP |
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-Related structure data
Related structure data | 3fxhC 3fy6C 3if4C 3imoC 3jrtC C: citing same article (ref.) |
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Similar structure data | |
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: 20532.076 Da / Num. of mol.: 3 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: B0BGB0 #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.75 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M ammonium sulfate, 25% PEG 3350 pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2→92.85 Å / Num. obs: 35948 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 15.3 / Num. measured all: 202528 | ||||||||||||||||||
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.56 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→37.126 Å / Occupancy max: 1 / Occupancy min: 0.59 / FOM work R set: 0.83 / SU ML: 0.3 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.01 / σ(I): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.835 Å2 / ksol: 0.383 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.29 Å2 / Biso mean: 38.766 Å2 / Biso min: 18.86 Å2
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Refinement step | Cycle: LAST / Resolution: 2→37.126 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: 30
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