+Open data
-Basic information
Entry | Database: PDB / ID: 4u07 | ||||||
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Title | ATP bound to eukaryotic FIC domain containing protein | ||||||
Components | Adenosine monophosphate-protein transferase FICD | ||||||
Keywords | TRANSFERASE / TPR / FIC / ATP | ||||||
Function / homology | Function and homology information protein deadenylylation / protein adenylylhydrolase activity / AMPylase activity / protein adenylyltransferase / protein adenylylation / regulation of IRE1-mediated unfolded protein response / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / negative regulation of GTPase activity / response to unfolded protein / Hsp70 protein binding ...protein deadenylylation / protein adenylylhydrolase activity / AMPylase activity / protein adenylyltransferase / protein adenylylation / regulation of IRE1-mediated unfolded protein response / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / negative regulation of GTPase activity / response to unfolded protein / Hsp70 protein binding / response to endoplasmic reticulum stress / protein-folding chaperone binding / endoplasmic reticulum membrane / protein homodimerization activity / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å | ||||||
Authors | Cole, A.R. / Bunney, T.D. / Katan, M. | ||||||
Citation | Journal: Structure / Year: 2014 Title: Crystal structure of the human, FIC-domain containing protein HYPE and implications for its functions. Authors: Bunney, T.D. / Cole, A.R. / Broncel, M. / Esposito, D. / Tate, E.W. / Katan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u07.cif.gz | 146.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u07.ent.gz | 112.2 KB | Display | PDB format |
PDBx/mmJSON format | 4u07.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u07_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4u07_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4u07_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 4u07_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/4u07 ftp://data.pdbj.org/pub/pdb/validation_reports/u0/4u07 | HTTPS FTP |
-Related structure data
Related structure data | 4u04C 4u0sC 4u0uC 4u0zC 3cucS 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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Unit cell |
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-Components
#1: Protein | Mass: 39548.273 Da / Num. of mol.: 2 / Fragment: UNP residues 102-445 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FICD, HIP13, HYPE, UNQ3041/PRO9857 / Production host: Escherichia coli (E. coli) References: UniProt: Q9BVA6, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.24 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% peg 3350, 200mM Na K tartrate, 100mM Bist-Tris Propane 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.984 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 26, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→48.88 Å / Num. obs: 27626 / % possible obs: 98.1 % / Redundancy: 3 % / Biso Wilson estimate: 58.21 Å2 / Net I/σ(I): 7.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CUC Resolution: 2.64→48.88 Å / Cor.coef. Fo:Fc: 0.8303 / Cor.coef. Fo:Fc free: 0.8172 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.475 / SU Rfree Blow DPI: 0.292
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Displacement parameters | Biso mean: 70.13 Å2
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Refine analyze | Luzzati coordinate error obs: 0.362 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.64→48.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.64→2.74 Å / Total num. of bins used: 14
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