+Open data
-Basic information
Entry | Database: PDB / ID: 3frs | ||||||
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Title | Structure of human IST1(NTD) (residues 1-189)(p43212) | ||||||
Components | Uncharacterized protein KIAA0174 | ||||||
Keywords | PROTEIN BINDING / ESCRT / ESCRT-III / IST1 / Phosphoprotein | ||||||
Function / homology | Function and homology information viral capsid secondary envelopment / MIT domain binding / abscission / ESCRT III complex disassembly / cytoskeleton-dependent cytokinesis / collateral sprouting / Sealing of the nuclear envelope (NE) by ESCRT-III / positive regulation of collateral sprouting / multivesicular body assembly / Flemming body ...viral capsid secondary envelopment / MIT domain binding / abscission / ESCRT III complex disassembly / cytoskeleton-dependent cytokinesis / collateral sprouting / Sealing of the nuclear envelope (NE) by ESCRT-III / positive regulation of collateral sprouting / multivesicular body assembly / Flemming body / positive regulation of proteolysis / endoplasmic reticulum-Golgi intermediate compartment / viral release from host cell / establishment of protein localization / protein localization / azurophil granule lumen / protein transport / nuclear envelope / midbody / cadherin binding / protein domain specific binding / cell division / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / chromatin / protein-containing complex binding / extracellular exosome / extracellular region / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.61 Å | ||||||
Authors | Schubert, H.L. / Hill, C.P. / Bajorek, M. / Sundquist, W.I. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2009 Title: Structural basis for ESCRT-III protein autoinhibition. Authors: Bajorek, M. / Schubert, H.L. / McCullough, J. / Langelier, C. / Eckert, D.M. / Stubblefield, W.M. / Uter, N.T. / Myszka, D.G. / Hill, C.P. / Sundquist, W.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3frs.cif.gz | 49.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3frs.ent.gz | 34.8 KB | Display | PDB format |
PDBx/mmJSON format | 3frs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3frs_validation.pdf.gz | 433.4 KB | Display | wwPDB validaton report |
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Full document | 3frs_full_validation.pdf.gz | 436.8 KB | Display | |
Data in XML | 3frs_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 3frs_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/3frs ftp://data.pdbj.org/pub/pdb/validation_reports/fr/3frs | HTTPS FTP |
-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: 21625.352 Da / Num. of mol.: 1 / Fragment: UNP residues 1-189 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IST1, KIAA0174 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon+RIL / References: UniProt: P53990 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.61 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10mM Tris-HCL, pH 8.0, 350mM NaCl, 1mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-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 |
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Reflection | Redundancy: 6.7 % / Av σ(I) over netI: 13.47 / Number: 40152 / Rmerge(I) obs: 0.074 / Χ2: 1 / D res high: 3.4 Å / D res low: 40 Å / Num. obs: 5970 / % possible obs: 88.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.61→50 Å / Num. all: 8387 / Num. obs: 8387 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 84.2 Å2 / Rmerge(I) obs: 0.079 / Χ2: 1.031 / Net I/σ(I): 13.47 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD | ||||||||||||||||||||||||||||
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Phasing set |
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Phasing MAD set |
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Phasing MAD set site |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.61→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.321 / WRfactor Rwork: 0.292 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.695 / SU B: 16.758 / SU ML: 0.305 / SU R Cruickshank DPI: 0.576 / SU Rfree: 0.341 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.576 / ESU R Free: 0.341 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.21 Å2 / Biso mean: 86.846 Å2 / Biso min: 36.15 Å2
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Refinement step | Cycle: LAST / Resolution: 2.61→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.61→2.676 Å / Total num. of bins used: 20
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