+Open data
-Basic information
Entry | Database: PDB / ID: 4gmo | ||||||
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Title | Crystal structure of Syo1 | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | CHAPERONE / ARM / HEAT / solenoid / nuclear transport / Rpl5 / Rpl11 / Kap104 / nucleus | ||||||
Function / homology | Function and homology information ribosomal large subunit biogenesis / protein import into nucleus / unfolded protein binding Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Bange, G. / Sinning, I. | ||||||
Citation | Journal: Science / Year: 2012 Title: Synchronizing nuclear import of ribosomal proteins with ribosome assembly. Authors: Kressler, D. / Bange, G. / Ogawa, Y. / Stjepanovic, G. / Bradatsch, B. / Pratte, D. / Amlacher, S. / Strauss, D. / Yoneda, Y. / Katahira, J. / Sinning, I. / Hurt, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gmo.cif.gz | 124.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gmo.ent.gz | 96 KB | Display | PDB format |
PDBx/mmJSON format | 4gmo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/4gmo ftp://data.pdbj.org/pub/pdb/validation_reports/gm/4gmo | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 75682.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0033460, Syo1 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: G0S5S6 |
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#2: 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: 2.26 Å3/Da / Density % sol: 45.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.7 Details: 0.2 M potassium acetate, 20% (v/v) PEG 3350, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 23, 2011 |
Radiation | Monochromator: horizontally diffracting Si (111) monochromator and Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→41.2 Å / Num. obs: 39669 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.6 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40.45 Å / SU ML: 0.29 / σ(F): 0 / Phase error: 25.07 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.674 Å2 / ksol: 0.361 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→40.45 Å
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Refine LS restraints |
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LS refinement shell |
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