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Yorodumi- PDB-6k8q: Solution structure of the intermembrane space domain of the mitoc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k8q | |||||||||
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Title | Solution structure of the intermembrane space domain of the mitochondrial import protein Tim21 from S. cerevisiae | |||||||||
Components | Mitochondrial import inner membrane translocase subunit TIM21 | |||||||||
Keywords | PROTEIN TRANSPORT / membrane / mitochondria / translocation | |||||||||
Function / homology | Function and homology information TIM23 mitochondrial import inner membrane translocase complex / protein import into mitochondrial matrix / protein insertion into mitochondrial inner membrane / mitochondrial inner membrane / mitochondrion Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
Authors | Bala, S. / Shinya, S. / Srivastava, A. / Shimada, A. / Kobayashi, N. / Kojima, C. / Tama, F. / Miyashita, O. / Kohda, D. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Biochim Biophys Acta Gen Subj / Year: 2020 Title: Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study. Authors: Bala, S. / Shinya, S. / Srivastava, A. / Ishikawa, M. / Shimada, A. / Kobayashi, N. / Kojima, C. / Tama, F. / Miyashita, O. / Kohda, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k8q.cif.gz | 857.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k8q.ent.gz | 728 KB | Display | PDB format |
PDBx/mmJSON format | 6k8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k8q_validation.pdf.gz | 534.6 KB | Display | wwPDB validaton report |
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Full document | 6k8q_full_validation.pdf.gz | 736.9 KB | Display | |
Data in XML | 6k8q_validation.xml.gz | 59.7 KB | Display | |
Data in CIF | 6k8q_validation.cif.gz | 78.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/6k8q ftp://data.pdbj.org/pub/pdb/validation_reports/k8/6k8q | HTTPS FTP |
-Related structure data
Related structure data | 6k7dC 6k7eC 6k7fC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13571.599 Da / Num. of mol.: 1 / Fragment: intermembrane space domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: TIM21, YGR033C / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P53220 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 323 uM [U-13C; U-15N] Tim21, 20 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O Label: 13C15N_sample / Solvent system: 90% H2O/10% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 50 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 300 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |