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Yorodumi- PDB-7qhy: Structure of a Kluyveromyces lactis protein involved in RNA decay -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qhy | ||||||
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Title | Structure of a Kluyveromyces lactis protein involved in RNA decay | ||||||
Components | Nonsense-mediated decay protein 4,Nonsense-mediated decay protein 4,Nonsense mediated mRNA decay protein 4 (Nmd4) | ||||||
Keywords | RNA BINDING PROTEIN / RNA decay / PIN domain / AlphaFold model / RoseTTAFold model | ||||||
Function / homology | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cytoplasm / Nonsense-mediated decay protein 4 Function and homology information | ||||||
Biological species | Kluyveromyces lactis (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Barbarin-Bocahu, I. / Graille, M. | ||||||
Funding support | France, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 Title: The X-ray crystallography phase problem solved thanks to AlphaFold and RoseTTAFold models: a case-study report. Authors: Barbarin-Bocahu, I. / Graille, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qhy.cif.gz | 165.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qhy.ent.gz | 131.6 KB | Display | PDB format |
PDBx/mmJSON format | 7qhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qhy_validation.pdf.gz | 430 KB | Display | wwPDB validaton report |
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Full document | 7qhy_full_validation.pdf.gz | 435.1 KB | Display | |
Data in XML | 7qhy_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 7qhy_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/7qhy ftp://data.pdbj.org/pub/pdb/validation_reports/qh/7qhy | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28696.729 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces lactis (yeast) Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: NMD4, KLLA0B08107g, KDRO_E07780 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CVZ8 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.63 Å3/Da / Density % sol: 53.16 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium citrate pH 5.6, 0.9-1 M Li2SO4 and 0.6 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97856 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→43.77 Å / Num. obs: 22619 / % possible obs: 99.8 % / Redundancy: 59.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0115 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 2.45→2.51 Å / Rmerge(I) obs: 3.897 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1648 / CC1/2: 0.605 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AlphaFold model Resolution: 2.45→43.76 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 0.301 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.299 / SU Rfree Blow DPI: 0.237 / SU Rfree Cruickshank DPI: 0.24
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Displacement parameters | Biso mean: 94.56 Å2
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Refine analyze | Luzzati coordinate error obs: 0.38 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→43.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.47 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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