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Yorodumi- PDB-3if4: Structure from the mobile metagenome of North West Arm Sewage Out... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3if4 | ||||||
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Title | Structure from the mobile metagenome of North West Arm Sewage Outfall: Integron Cassette Protein Hfx_Cass5 | ||||||
Components | Integron Cassette Protein Hfx_Cass5 | ||||||
Keywords | structural genomics / unknown function / Integron Cassette Protein Mobile Metagenome Structural Genomics PSI-2 Protein Structure Initiative Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Integron cassette protein helical domain / Integron cassette protein / Anthopleurin-A / Single Sheet / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Beta / Mainly Alpha Function and homology information | ||||||
Biological species | unidentified (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.181 Å | ||||||
Authors | Sureshan, V. / Deshpande, C.N. / Harrop, S.J. / Evdokimova, E. / Kudrytska, M. / Koenig, J.E. / Osipiuk, J. / Edwards, A. / Savchenko, A. / Joachimiak, A. ...Sureshan, V. / Deshpande, C.N. / Harrop, S.J. / Evdokimova, E. / Kudrytska, M. / Koenig, J.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. / 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 | 3if4.cif.gz | 170.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3if4.ent.gz | 143.1 KB | Display | PDB format |
PDBx/mmJSON format | 3if4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3if4_validation.pdf.gz | 444.4 KB | Display | wwPDB validaton report |
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Full document | 3if4_full_validation.pdf.gz | 449 KB | Display | |
Data in XML | 3if4_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 3if4_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/3if4 ftp://data.pdbj.org/pub/pdb/validation_reports/if/3if4 | HTTPS FTP |
-Related structure data
Related structure data | 3fuyC 3fxhC 3fy6C 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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2 |
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Unit cell |
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Details | The four chains in the asymmetric unit arrange as two dimers. Dimer 1: Chain A and Chain C Dimer 2: Chain B and Chain D |
-Components
#1: Protein | Mass: 13649.657 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: uncultured bacterium / Source: (gene. exp.) unidentified (others) / Plasmid: p15TV LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPlus(DE3)-RIPL #2: 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: 1.94 Å3/Da / Density % sol: 36.53 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 29% PEG3350, 0.1 M Hepes pH 7.5, 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-ID / Wavelength: 0.9798 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 5, 2009 |
Radiation | Monochromator: 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: 2.18→50 Å / Num. obs: 21618 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 34.6 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 4 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 2.62 / Rsym value: 0.531 / % possible all: 68.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.181→40.226 Å / SU ML: 0.3 / Isotropic thermal model: anisotropic / σ(F): 0.05 / Phase error: 24.86 / 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: 50.641 Å2 / ksol: 0.359 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.181→40.226 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection details: chain D and (resseq 53:98)) |