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Yorodumi- PDB-6g81: Solution structure of the Ni metallochaperone HypA from Helicobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g81 | ||||||
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Title | Solution structure of the Ni metallochaperone HypA from Helicobacter pylori | ||||||
Components | Hydrogenase maturation factor HypA | ||||||
Keywords | METAL BINDING PROTEIN / metallochaperone metal-binding Nickel hydrogenase | ||||||
Function / homology | Function and homology information protein modification process => GO:0036211 / nickel cation binding / protein maturation / zinc ion binding Similarity search - Function | ||||||
Biological species | Helicobacter pylori J99 (bacteria) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Spronk, C.A.E.M. / Zerko, S. / Gorka, M. / Kozminski, W. / Bardiaux, B. / Zambelli, B. / Musiani, F. / Piccioli, M. / Hu, H. / Maroney, M. / Ciurli, S. | ||||||
Citation | Journal: J. Biol. Inorg. Chem. / Year: 2018 Title: Structure and dynamics of Helicobacter pylori nickel-chaperone HypA: an integrated approach using NMR spectroscopy, functional assays and computational tools. Authors: Spronk, C.A.E.M. / Zerko, S. / Gorka, M. / Kozminski, W. / Bardiaux, B. / Zambelli, B. / Musiani, F. / Piccioli, M. / Basak, P. / Blum, F.C. / Johnson, R.C. / Hu, H. / Merrell, D.S. / Maroney, M. / Ciurli, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g81.cif.gz | 716.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g81.ent.gz | 598.9 KB | Display | PDB format |
PDBx/mmJSON format | 6g81.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g81_validation.pdf.gz | 546.8 KB | Display | wwPDB validaton report |
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Full document | 6g81_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6g81_validation.xml.gz | 239.4 KB | Display | |
Data in CIF | 6g81_validation.cif.gz | 171.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/6g81 ftp://data.pdbj.org/pub/pdb/validation_reports/g8/6g81 | HTTPS FTP |
-Related structure data
Similar structure data | |
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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: 13221.247 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori J99 (bacteria) / Strain: J99 / ATCC 700824 / Gene: hypA, jhp_0803 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0U5 |
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#2: Chemical | ChemComp-ZN / |
-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-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O Label: 13C15N_sample / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Details: Protein samples for NMR spectroscopy were constituted by ca. 1 mM [15N/13C]-labeled apo-HpHypA in 20 mM HEPES at pH 7.2 (or pH 6.3), 200 mM NaCl, 1 mM TCEP Ionic strength: 0.2 Not defined / Label: condition_1 / pH: 7.2 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 7 | |||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | |||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |