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Yorodumi- PDB-6ap0: Crystal structure of human FLASH N-terminal domain C54S/C83A (Cry... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ap0 | ||||||
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Title | Crystal structure of human FLASH N-terminal domain C54S/C83A (Crystal form 2) | ||||||
Components | CASP8-associated protein 2 | ||||||
Keywords | GENE REGULATION / coiled-coil | ||||||
Function / homology | Function and homology information Fas signaling pathway / SUMO polymer binding / peptidase activator activity involved in apoptotic process / death receptor binding / cysteine-type endopeptidase activator activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / SUMOylation of transcription cofactors / apoptotic signaling pathway / PML body / activation of cysteine-type endopeptidase activity involved in apoptotic process ...Fas signaling pathway / SUMO polymer binding / peptidase activator activity involved in apoptotic process / death receptor binding / cysteine-type endopeptidase activator activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / SUMOylation of transcription cofactors / apoptotic signaling pathway / PML body / activation of cysteine-type endopeptidase activity involved in apoptotic process / cellular response to mechanical stimulus / transcription corepressor activity / signal transduction / mitochondrion / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.581 Å | ||||||
Authors | Aik, W.S. / Tong, L. | ||||||
Citation | Journal: PLoS ONE / Year: 2017 Title: The N-terminal domains of FLASH and Lsm11 form a 2:1 heterotrimer for histone pre-mRNA 3'-end processing. Authors: Aik, W.S. / Lin, M.H. / Tan, D. / Tripathy, A. / Marzluff, W.F. / Dominski, Z. / Chou, C.Y. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ap0.cif.gz | 84.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ap0.ent.gz | 64.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ap0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ap0_validation.pdf.gz | 432.8 KB | Display | wwPDB validaton report |
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Full document | 6ap0_full_validation.pdf.gz | 434.6 KB | Display | |
Data in XML | 6ap0_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 6ap0_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/6ap0 ftp://data.pdbj.org/pub/pdb/validation_reports/ap/6ap0 | HTTPS FTP |
-Related structure data
Related structure data | 6anoSC 6aozC 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: 11333.769 Da / Num. of mol.: 2 / Fragment: UNP residues 51-137 / Mutation: C54S, C83A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP8AP2, FLASH, KIAA1315, RIP25 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKL3 #2: 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: 2.1 Å3/Da / Density % sol: 41.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM sodium formate, 15% (w/v) PEG 3350, 3% (v/v) 1,6-hexanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→36.216 Å / Num. obs: 11542 / % possible obs: 99.6 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.42 |
Reflection shell | Resolution: 2.58→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 3.82 / Num. unique obs: 1848 / CC1/2: 0.898 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ANO Resolution: 2.581→36.216 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.581→36.216 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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