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Yorodumi- PDB-5lam: Refined 3D NMR structure of the cytoplasmic rhodanese domain of t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lam | ||||||||||||
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Title | Refined 3D NMR structure of the cytoplasmic rhodanese domain of the inner membrane protein YgaP from Escherichia coli | ||||||||||||
Components | Inner membrane protein YgaP | ||||||||||||
Keywords | MEMBRANE PROTEIN / Rhodanese domain of YgaP / PROTEIN | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | SOLUTION NMR / Energy refinement | ||||||||||||
Authors | Eichmann, C. / Tzitzilonis, C. / Nakamura, T. / Maslennikov, I. / Kwiatkowski, W. / Choe, S. / Lipton, S.A. / Guntert, P. / Riek, R. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Mol.Biol. / Year: 2016 Title: S-Nitrosylation Induces Structural and Dynamical Changes in a Rhodanese Family Protein. Authors: Eichmann, C. / Tzitzilonis, C. / Nakamura, T. / Kwiatkowski, W. / Maslennikov, I. / Choe, S. / Lipton, S.A. / Riek, R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lam.cif.gz | 641.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lam.ent.gz | 536.9 KB | Display | PDB format |
PDBx/mmJSON format | 5lam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/5lam ftp://data.pdbj.org/pub/pdb/validation_reports/la/5lam | HTTPS FTP |
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-Related structure data
Related structure data | 5hblC 5hboC 5hbpC 5hbqC 5laoC C: citing same article (ref.) |
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Similar structure data | |
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: 11716.311 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: ygaP, b2668, JW2643 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS Star / References: UniProt: P55734 |
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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: 1 mM [U-99% 13C; U-99% 15N] Rhodanese domain, 95% H2O/5% D2O Label: Rhodanese / Solvent system: 95% H2O/5% D2O |
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Sample | Conc.: 1 mM / Component: Rhodanese domain / Isotopic labeling: [U-99% 13C; U-99% 15N] |
Sample conditions | Ionic strength: 0 mM / Label: Rhodanese / pH: 7 / Pressure: AMBIENT Pa / Temperature: 303.15 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz |
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-Processing
NMR software |
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Refinement | Method: Energy refinement / Software ordinal: 1 | ||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |