+Open data
-Basic information
Entry | Database: PDB / ID: 8jkr | ||||||
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Title | SP1746 in complex with UMP | ||||||
Components | 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 serotype 4 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 | 8jkr.cif.gz | 59.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jkr.ent.gz | 40.6 KB | Display | PDB format |
PDBx/mmJSON format | 8jkr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jkr_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 8jkr_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 8jkr_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 8jkr_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/8jkr ftp://data.pdbj.org/pub/pdb/validation_reports/jk/8jkr | HTTPS FTP |
-Related structure data
Related structure data | 8jjaC 8jjkC 8jk5C 8jk8C 8jk9C 8jkaC 8jkpC 8yt5C 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25051.236 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria) Gene: SP_1746 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0H2URF8, bis(5'-nucleosyl)-tetraphosphatase (symmetrical) |
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-Non-polymers , 6 types, 130 molecules
#2: Chemical | ChemComp-U5P / | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.48 Å3/Da / Density % sol: 50.31 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, sitting drop / Details: 25% PEG4000, 0.15 M (NH4)2SO4, 0.1 M MES, 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: 0.97852 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 26, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 2→50.01 Å / Num. obs: 17261 / % possible obs: 99.9 % / Redundancy: 9.6 % / CC1/2: 0.999 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 2→2.05 Å / Num. unique obs: 1266 / CC1/2: 0.979 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.663 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.302 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.149 / 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: 43.262 Å2
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Refinement step | Cycle: 1 / Resolution: 2→19.663 Å
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Refine LS restraints |
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