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- PDB-6y9u: Crystal structure of PnrA from S. pneumoniae in complex with adenosine -
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Open data
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Basic information
Entry | Database: PDB / ID: 6y9u | ||||||
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Title | Crystal structure of PnrA from S. pneumoniae in complex with adenosine | ||||||
![]() | Lipoprotein | ||||||
![]() | TRANSPORT PROTEIN / Nucleoside substrate-binding protein | ||||||
Function / homology | ABC transporter substrate-binding protein PnrA-like / ABC transporter substrate-binding protein PnrA-like / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / plasma membrane / ACETATE ION / ADENOSINE / NICKEL (II) ION / Lipoprotein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Batuecas, M.T. / Hermoso, J.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure and Pathophysiological Role of the Pneumococcal Nucleoside-binding Protein PnrA. Authors: Abdullah, M.R. / Batuecas, M.T. / Jennert, F. / Voss, F. / Westhoff, P. / Kohler, T.P. / Molina, R. / Hirschmann, S. / Lalk, M. / Hermoso, J.A. / Hammerschmidt, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 264 KB | Display | ![]() |
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PDB format | ![]() | 212.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 810.1 KB | Display | ![]() |
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Full document | ![]() | 821.7 KB | Display | |
Data in XML | ![]() | 48.8 KB | Display | |
Data in CIF | ![]() | 68.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ya3C ![]() 6ya4C ![]() 6yabC ![]() 6yagC ![]() 2fqwS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 35184.699 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-NI / #3: Chemical | ChemComp-ADN / #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 28% PEG 600, 0.2 M calcium acetate and 0.1 M sodium cacodylate (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→49.06 Å / Num. obs: 50919 / % possible obs: 99.88 % / Redundancy: 11.3 % / CC1/2: 0.99 / Rpim(I) all: 0.04 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.5→2.56 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3737 / CC1/2: 0.74 / Rpim(I) all: 0.36 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2FQW Resolution: 2.5→49.06 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso max: 139.29 Å2 / Biso mean: 56.9129 Å2 / Biso min: 20.58 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→49.06 Å
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