+Open data
-Basic information
Entry | Database: PDB / ID: 8yt5 | ||||||
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Title | SP1746 treated with EDTA, in complex with ADP | ||||||
Components | bis(5'-nucleosyl)-tetraphosphatase (symmetrical)Bis(5'-nucleosyl)-tetraphosphatase (symmetrical) | ||||||
Keywords | HYDROLASE / enzyme / HD domain superfamily protein / phosphohydrolase / unknown gene product / SP1746 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pneumoniae TIGR4 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Jin, Y. / Niu, L. / Ke, J. | ||||||
Funding support | 1items
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Citation | Journal: Structure / Year: 2024 Title: Structural and biochemical characterization of a nucleotide hydrolase from Streptococcus pneumonia. Authors: Jin, Y. / Ke, J. / Zheng, P. / Zhang, H. / Zhu, Z. / Niu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8yt5.cif.gz | 61 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yt5.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 8yt5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/8yt5 ftp://data.pdbj.org/pub/pdb/validation_reports/yt/8yt5 | HTTPS FTP |
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-Related structure data
Related structure data | 8jjaC 8jjkC 8jk5C 8jk8C 8jk9C 8jkaC 8jkpC 8jkrC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25051.236 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria) Strain: ATCC BAA-334 / TIGR4 / Gene: SP_1746 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0H2URF8, bis(5'-nucleosyl)-tetraphosphatase (symmetrical) | ||||
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#2: Chemical | ChemComp-ADP / | ||||
#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: 2.45 Å3/Da / Density % sol: 49.71 % |
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Crystal grow | Temperature: 287.2 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350,0.2 M Potassium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.98405 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 28, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98405 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50.01 Å / Num. obs: 32997 / % possible obs: 100 % / Redundancy: 19.1 % / CC1/2: 0.9993 / Net I/σ(I): 31.97 |
Reflection shell | Resolution: 1.6→1.64 Å / Num. unique obs: 2407 / CC1/2: 0.8428 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→50.01 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.409 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 19.827 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→50.01 Å
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Refine LS restraints |
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