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- PDB-6yab: Crystal structure of PnrA from S. pneumoniae in complex with uridine -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yab | ||||||
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Title | Crystal structure of PnrA from S. pneumoniae in complex with uridine | ||||||
![]() | (Lipoprotein) x 3 | ||||||
![]() | TRANSPORT PROTEIN / Nucleoside substrate-binding protein | ||||||
Function / homology | ![]() | ||||||
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 | ![]() | 277.9 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 502.4 KB | Display | ![]() |
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Full document | ![]() | 520 KB | Display | |
Data in XML | ![]() | 49.2 KB | Display | |
Data in CIF | ![]() | 68.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6y9uC ![]() 6ya3C ![]() 6ya4C ![]() 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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1 | ![]()
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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
-Protein , 3 types, 4 molecules CCCBBBAAADDD
#1: Protein | Mass: 35127.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: SP_0845 / Production host: ![]() ![]() #2: Protein | | Mass: 34953.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: SP_0845 / Production host: ![]() ![]() #3: Protein | | Mass: 34998.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: SP_0845 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 309 molecules ![](data/chem/img/NI.gif)
![](data/chem/img/URI.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/URI.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-NI / #5: Chemical | ChemComp-URI / #6: Chemical | ChemComp-CAC / | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.86 % |
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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: Nov 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97895 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→49.135 Å / Num. obs: 68314 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.99 / Rpim(I) all: 0.03 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.3→2.35 Å / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4545 / CC1/2: 0.93 / Rpim(I) all: 0.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2FQW Resolution: 2.3→49.09 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.3→49.09 Å
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