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Yorodumi- PDB-8ucy: Sterile Alpha Motif (SAM) domain from Tric1, Arabidopsis thaliana -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ucy | ||||||
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Title | Sterile Alpha Motif (SAM) domain from Tric1, Arabidopsis thaliana | ||||||
Components | Chloroplastic import inner membrane translocase subunit HP30-1 | ||||||
Keywords | RNA BINDING PROTEIN / Mitochondria / tRNA import / Tric1 / SAM domain / oligomerization / PRAT domain / sterile alpha motif domain | ||||||
Function / homology | Function and homology information tRNA import into mitochondrion / protein targeting to chloroplast / chloroplast inner membrane / protein insertion into mitochondrial inner membrane / chloroplast envelope / plastid / protein transmembrane transporter activity / mitochondrion organization / chloroplast / : ...tRNA import into mitochondrion / protein targeting to chloroplast / chloroplast inner membrane / protein insertion into mitochondrial inner membrane / chloroplast envelope / plastid / protein transmembrane transporter activity / mitochondrion organization / chloroplast / : / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.48 Å | ||||||
Authors | Olasz, B. / Vrielink, A. / Evans, G.L. | ||||||
Funding support | 1items
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Citation | Journal: J.Biol.Chem. / Year: 2024 Title: Structural analysis of the SAM domain of the Arabidopsis mitochondrial tRNA import receptor. Authors: Olasz, B. / Smithers, L. / Evans, G.L. / Anandan, A. / Murcha, M.W. / Vrielink, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ucy.cif.gz | 147.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ucy.ent.gz | 105 KB | Display | PDB format |
PDBx/mmJSON format | 8ucy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ucy_validation.pdf.gz | 445.7 KB | Display | wwPDB validaton report |
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Full document | 8ucy_full_validation.pdf.gz | 446.4 KB | Display | |
Data in XML | 8ucy_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 8ucy_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/8ucy ftp://data.pdbj.org/pub/pdb/validation_reports/uc/8ucy | HTTPS FTP |
-Related structure data
Related structure data | 8uczC 8ud0C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | The assembly may be hexameric; however, the authors do not know the specific hexameric assembly. |
-Components
#1: Protein | Mass: 10165.782 Da / Num. of mol.: 3 / Fragment: SAM domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HP30-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: Q9SCK3 #2: Chemical | ChemComp-CL / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal |
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Crystal grow |
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-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 | Resolution: 1.48→29.2 Å / Num. obs: 42224 / % possible obs: 99.9 % / Redundancy: 14.3 % / Biso Wilson estimate: 19.28 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.015 / Net I/σ(I): 28.1 | ||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.48→1.51 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2085 / CC1/2: 0.671 / Rpim(I) all: 0.403 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.48→29.17 Å / SU ML: 0.1539 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9588 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: The structure was solved by MAD using a SeMet mutant; however, the final refined structure was obtained using a native data set.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→29.17 Å
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Refine LS restraints |
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LS refinement shell |
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