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Yorodumi- PDB-7d8q: The structure of nucleotide phosphatase Sa1684 complex with GDP a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d8q | ||||||
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Title | The structure of nucleotide phosphatase Sa1684 complex with GDP analogue from Staphylococcus aureus | ||||||
Components | UPF0374 protein SAB1800c | ||||||
Keywords | CYTOSOLIC PROTEIN / nucleitide phosphatase | ||||||
Function / homology | Uncharacterised protein family UPF0374 / Domain of unknown function DUF402 / FomD-like superfamily / Protein of unknown function (DUF402) / Chem-GZF / UPF0374 protein SAB1800c Function and homology information | ||||||
Biological species | Staphylococcus aureus RF122 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Wang, Z. / Li, X. | ||||||
Funding support | China, 1items
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Citation | Journal: Febs J. / Year: 2021 Title: The structural mechanism for the nucleoside tri- and diphosphate hydrolysis activity of Ntdp from Staphylococcus aureus. Authors: Wang, Z. / Shen, H. / He, B. / Teng, M. / Guo, Q. / Li, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d8q.cif.gz | 51.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d8q.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 7d8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/7d8q ftp://data.pdbj.org/pub/pdb/validation_reports/d8/7d8q | HTTPS FTP |
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-Related 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: 21734.592 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus RF122 (bacteria) / Strain: bovine RF122 / ET3-1 / Gene: SAB1800c / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YU19 | ||||
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#2: Chemical | ChemComp-GZF / [( | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.53 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 20%PEG400, 0.1M sodium citrate pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9875 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9875 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 30428 / % possible obs: 98.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.8 |
Reflection shell | Resolution: 1.5→1.53 Å / Num. unique obs: 1505 / CC1/2: 0.936 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→30.19 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1903 / WRfactor Rwork: 0.1672 / FOM work R set: 0.8749 / SU B: 1.216 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0679 / SU Rfree: 0.0678 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.84 Å2 / Biso mean: 16.503 Å2 / Biso min: 7.77 Å2
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Refinement step | Cycle: final / Resolution: 1.5→30.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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