+Open data
-Basic information
Entry | Database: PDB / ID: 3fm0 | ||||||
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Title | Crystal structure of WD40 protein Ciao1 | ||||||
Components | Protein CIAO1 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / WDR39 / SGC / WD40 / Ciao1 / Nucleus / WD repeat / Structural Genomics / Structural Genomics Consortium | ||||||
Function / homology | Function and homology information cytosolic [4Fe-4S] assembly targeting complex / protein maturation by iron-sulfur cluster transfer / MMXD complex / Cytosolic iron-sulfur cluster assembly / iron-sulfur cluster assembly / chromosome segregation / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Dong, A. / Ravichandran, M. / Crombet, L. / Cossar, D. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. ...Dong, A. / Ravichandran, M. / Crombet, L. / Cossar, D. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. / Ouyang, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Protein Cell / Year: 2011 Title: Structure and function of WD40 domain proteins. Authors: Xu, C. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fm0.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fm0.ent.gz | 62.6 KB | Display | PDB format |
PDBx/mmJSON format | 3fm0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/3fm0 ftp://data.pdbj.org/pub/pdb/validation_reports/fm/3fm0 | HTTPS FTP |
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-Related structure data
Related structure data | 3e0cC 3gfcC 3i2nC 3ow8C 2hesS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 38707.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CIAO1, WDR39 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta-R3 / References: UniProt: O76071 |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 1.92 Å3/Da / Density % sol: 35.95 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 25% PEG 3350, 0.1M (NH4)2SO4, 0.1M Bis-tris, pH6.0, 8% 2,2,2-trifluro ethanol, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 30710 / Num. obs: 30710 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 2.62 / Num. unique all: 1055 / Rsym value: 0.421 / % possible all: 66.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2HES Resolution: 1.7→47.78 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.057 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.112 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.727 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→47.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.702→1.746 Å / Total num. of bins used: 20
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