+Open data
-Basic information
Entry | Database: PDB / ID: 6xh9 | ||||||||||||
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Title | Crystal structure of S. aureus TarJ | ||||||||||||
Components | Ribulose-5-phosphate reductase 1 | ||||||||||||
Keywords | OXIDOREDUCTASE / alcohol dehydrogenase | ||||||||||||
Function / homology | Function and homology information ribitol-5-phosphate 2-dehydrogenase (NADP+) / ribitol-5-phosphate 2-dehydrogenase [(NAD(P)+] activity / poly(ribitol phosphate) teichoic acid biosynthetic process / cell wall organization / zinc ion binding Similarity search - Function | ||||||||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||||||||
Authors | Li, F.K.K. / Strynadka, N.C.J. | ||||||||||||
Funding support | Canada, 3items
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Citation | Journal: J.Struct.Biol. / Year: 2021 Title: Crystallographic analysis of TarI and TarJ, a cytidylyltransferase and reductase pair for CDP-ribitol synthesis in Staphylococcus aureus wall teichoic acid biogenesis. Authors: Li, F.K.K. / Gale, R.T. / Petrotchenko, E.V. / Borchers, C.H. / Brown, E.D. / Strynadka, N.C.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xh9.cif.gz | 137.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xh9.ent.gz | 106.6 KB | Display | PDB format |
PDBx/mmJSON format | 6xh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xh9_validation.pdf.gz | 428.2 KB | Display | wwPDB validaton report |
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Full document | 6xh9_full_validation.pdf.gz | 431.8 KB | Display | |
Data in XML | 6xh9_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 6xh9_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/6xh9 ftp://data.pdbj.org/pub/pdb/validation_reports/xh/6xh9 | HTTPS FTP |
-Related structure data
Related structure data | 6xhkC 6xhpC 6xhqC 6xhrC 6xhsC 6xhtC 4ilkS 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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Unit cell |
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-Components
#1: Protein | Mass: 38565.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: tarJ, SAOUHSC_00226 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q2G1B9, ribitol-5-phosphate 2-dehydrogenase (NADP+) |
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Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.97 Å3/Da / Density % sol: 75.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 1.1 M ammonium phosphate monobasic, 0.1 M sodium citrate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→48.909 Å / Num. obs: 13739 / % possible obs: 99.88 % / Redundancy: 18.9 % / CC1/2: 0.999 / Rpim(I) all: 0.05771 / Net I/σ(I): 13.44 |
Reflection shell | Resolution: 3.2→3.315 Å / Mean I/σ(I) obs: 1.46 / Num. unique obs: 1340 / CC1/2: 0.698 / Rpim(I) all: 0.5733 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ILK Resolution: 3.2→48.909 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 195.46 Å2 / Biso mean: 109.3954 Å2 / Biso min: 68.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→48.909 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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