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Yorodumi- PDB-4zn4: Crystal structure of Sqt1 from Chaetomium thermophilum solved by MR -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zn4 | ||||||
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Title | Crystal structure of Sqt1 from Chaetomium thermophilum solved by MR | ||||||
Components | sqt1HERG | ||||||
Keywords | CHAPERONE / ribosome biogenesis | ||||||
Function / homology | Function and homology information YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å | ||||||
Authors | Ahmed, Y.L. / Sinning, I. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Co-translational capturing of nascent ribosomal proteins by their dedicated chaperones. Authors: Pausch, P. / Singh, U. / Ahmed, Y.L. / Pillet, B. / Murat, G. / Altegoer, F. / Stier, G. / Thoms, M. / Hurt, E. / Sinning, I. / Bange, G. / Kressler, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zn4.cif.gz | 321.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zn4.ent.gz | 262 KB | Display | PDB format |
PDBx/mmJSON format | 4zn4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/4zn4 ftp://data.pdbj.org/pub/pdb/validation_reports/zn/4zn4 | HTTPS FTP |
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-Related structure data
Related structure data | 4zovC 4zoxC 4zoyC 4zozC 3ow8S C: citing same article (ref.) S: Starting model for refinement |
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Similar 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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-Components
#1: Protein | Mass: 57033.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0010920 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: G0S0R0 #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: 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: 2.07 Å3/Da / Density % sol: 40.58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.6M (NH4)2SO4 and 100 mM MES pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.60508 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.60508 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.94→47.41 Å / Num. obs: 67775 / % possible obs: 98.6 % / Redundancy: 4.8 % / Biso Wilson estimate: 33.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.027 / Net I/σ(I): 14.6 / Num. measured all: 325940 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ow8 Resolution: 1.94→47.411 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.82 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→47.411 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 19.4545 Å / Origin y: 71.0445 Å / Origin z: 22.705 Å
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Refinement TLS group | Selection details: all |