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Yorodumi- PDB-6ya4: Crystal structure of PnrA from S. pneumoniae in complex with cytidine -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ya4 | ||||||
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Title | Crystal structure of PnrA from S. pneumoniae in complex with cytidine | ||||||
Components | Lipoprotein | ||||||
Keywords | TRANSPORT PROTEIN / Nucleoside substrate-binding protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Batuecas, M.T. / Hermoso, J.A. | ||||||
Funding support | Spain, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ya4.cif.gz | 269.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ya4.ent.gz | 216.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ya4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ya4_validation.pdf.gz | 496 KB | Display | wwPDB validaton report |
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Full document | 6ya4_full_validation.pdf.gz | 512.8 KB | Display | |
Data in XML | 6ya4_validation.xml.gz | 53.2 KB | Display | |
Data in CIF | 6ya4_validation.cif.gz | 74.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/6ya4 ftp://data.pdbj.org/pub/pdb/validation_reports/ya/6ya4 | HTTPS FTP |
-Related structure data
Related structure data | 6y9uC 6ya3C 6yabC 6yagC 2fqwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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 , 1 types, 4 molecules CABD
#1: Protein | Mass: 35184.699 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: SP_0845 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2UPF3 |
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-Non-polymers , 5 types, 513 molecules
#2: Chemical | ChemComp-CTN / #3: Chemical | ChemComp-NI / #4: Chemical | ChemComp-ACT / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.09 % |
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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: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97895 Å |
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: 2.2→49.12 Å / Num. obs: 78306 / % possible obs: 99.7 % / Redundancy: 7.7 % / CC1/2: 0.99 / Rpim(I) all: 0.06 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.2→2.24 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4445 / CC1/2: 0.71 / Rpim(I) all: 0.62 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FQW Resolution: 2.2→49.07 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso max: 135.43 Å2 / Biso mean: 44.8793 Å2 / Biso min: 13.13 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→49.07 Å
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