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Yorodumi- PDB-6dt3: 1.2 Angstrom Resolution Crystal Structure of Nucleoside Triphosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dt3 | ||||||
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Title | 1.2 Angstrom Resolution Crystal Structure of Nucleoside Triphosphatase NudI from Klebsiella pneumoniae in Complex with HEPES | ||||||
Components | Nucleoside triphosphatase NudI | ||||||
Keywords | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / putative NUDIX hydrolase / HEPES | ||||||
Function / homology | Function and homology information dCTP diphosphatase / dTTP diphosphatase activity / dCTP diphosphatase activity / NADH pyrophosphatase activity / nucleotide diphosphatase / dUTP diphosphatase / dUTP diphosphatase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / magnesium ion binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Pshenychnyi, S. / Endres, M. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Microbiol Resour Announc / Year: 2023 Title: A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae. Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / ...Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / Anderson, W.F. / Hauser, A.R. / Joachimiak, A. / Satchell, K.J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dt3.cif.gz | 151.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dt3.ent.gz | 122.9 KB | Display | PDB format |
PDBx/mmJSON format | 6dt3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dt3_validation.pdf.gz | 443.5 KB | Display | wwPDB validaton report |
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Full document | 6dt3_full_validation.pdf.gz | 445.9 KB | Display | |
Data in XML | 6dt3_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 6dt3_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/6dt3 ftp://data.pdbj.org/pub/pdb/validation_reports/dt/6dt3 | HTTPS FTP |
-Related structure data
Related structure data | 6duxC 6dvvC 6dxnC 6e85C 6nauC 6nbgC 6ndiC 6wn5C 6wn8C 6x1lC 7rjjC 7tl5C 7tzpC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16653.455 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 (bacteria) Gene: nudI, B1727_21840 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 Gold References: UniProt: A0A1W1Q5B1, nucleotide diphosphatase, dCTP diphosphatase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides, dUTP diphosphatase #2: Chemical | ChemComp-EPE / | #3: Water | ChemComp-HOH / | |
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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: 2.18 Å3/Da / Density % sol: 43.6 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10.0 mg/mL protein, 0.5 M sodium chloride, 0.01 M Tris, pH 8.3 against Classics II (F8) (0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 25% w/v PEG3350) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 11, 2018 / Details: C(111) |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→30 Å / Num. obs: 78810 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.052 / Rrim(I) all: 0.088 / Rsym value: 0.07 / Χ2: 1.201 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3881 / CC1/2: 0.593 / Rpim(I) all: 0.563 / Rrim(I) all: 0.973 / Rsym value: 0.79 / Χ2: 1.003 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.2→27.14 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.771 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 16.812 Å2
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Refinement step | Cycle: 1 / Resolution: 1.2→27.14 Å
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Refine LS restraints |
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