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Yorodumi- PDB-2k8e: Solution NMR Structure of protein of unknown function yegP from E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2k8e | ||||||
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Title | Solution NMR Structure of protein of unknown function yegP from E. coli. Ontario Center for Structural Proteomics target EC0640_1_123 Northeast Structural Genomics Consortium Target ET102. | ||||||
Components | UPF0339 protein yegP | ||||||
Keywords | structural genomics / unknown function / YegP / Protein Structure initiative (PSI) / Northeast structural genomics consortium (NESG) / Ontario Centre for structural proteomics (OCSP) / Escherichia Coli | ||||||
Function / homology | PH-domain like - #80 / Domain of unknown function DUF1508 / Domain of unknown function (DUF1508) / YegP-like superfamily / PH-domain like / double-strand break repair / Roll / Mainly Beta / UPF0339 protein YegP Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Fares, C. / Lemak, A. / Gutmanas, A. / Karra, M. / Yee, A.H. / Semesi, A. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP) | ||||||
Citation | Journal: To be Published Title: Solution structure of protein yegP from Escherichia Coli. Authors: Fares, C. / Lemak, A. / Gutmanas, A. / Karra, M. / Yee, A. / Semesi, A. / Arrowsmith, C.H. #1: Journal: J.Biomol.Nmr / Year: 2011 Title: A novel strategy for NMR resonance assignment and protein structure determination. Authors: Lemak, A. / Gutmanas, A. / Chitayat, S. / Karra, M. / Fares, C. / Sunnerhagen, M. / Arrowsmith, C.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2k8e.cif.gz | 675.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2k8e.ent.gz | 569 KB | Display | PDB format |
PDBx/mmJSON format | 2k8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2k8e_validation.pdf.gz | 540.2 KB | Display | wwPDB validaton report |
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Full document | 2k8e_full_validation.pdf.gz | 748.2 KB | Display | |
Data in XML | 2k8e_validation.xml.gz | 60 KB | Display | |
Data in CIF | 2k8e_validation.cif.gz | 71.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/2k8e ftp://data.pdbj.org/pub/pdb/validation_reports/k8/2k8e | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 14237.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yegP, b2080, JW5339 / Plasmid: P11 / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: P76402 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: all experiments using non-uniform sampling |
-Sample preparation
Details | Contents: 0.5 mM [U-100% 13C; U-100% 15N] EC0640, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.5 mM / Component: EC0640 / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: 300 / pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / 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 |