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Yorodumi- PDB-7vtd: Unliganded structure of Pseudouridine kinase (PUKI) from Escheric... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vtd | ||||||
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Title | Unliganded structure of Pseudouridine kinase (PUKI) from Escherichia coli strain B | ||||||
Components | Pseudouridine kinase | ||||||
Keywords | TRANSFERASE / pseudouridine kinase / pseudourdine / pfkb family | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15054869646 Å | ||||||
Authors | Kim, S.H. / Rhee, S. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: Substrate-binding loop interactions with pseudouridine trigger conformational changes that promote catalytic efficiency of pseudouridine kinase PUKI. Authors: Kim, S.H. / Kim, M. / Park, D. / Byun, S. / Rhee, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vtd.cif.gz | 564 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vtd.ent.gz | 390.1 KB | Display | PDB format |
PDBx/mmJSON format | 7vtd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vtd_validation.pdf.gz | 454.5 KB | Display | wwPDB validaton report |
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Full document | 7vtd_full_validation.pdf.gz | 464.5 KB | Display | |
Data in XML | 7vtd_validation.xml.gz | 43.7 KB | Display | |
Data in CIF | 7vtd_validation.cif.gz | 60.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/7vtd ftp://data.pdbj.org/pub/pdb/validation_reports/vt/7vtd | HTTPS FTP |
-Related structure data
Related structure data | 7vteC 7vtfC 7vtgC 7vvaC 3kzhS S: Starting model for refinement 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 3 - 308 / Label seq-ID: 3 - 308
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-Components
#1: Protein | Mass: 33781.094 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: psuK, psuK_1, psuK_2, A8C65_16945, BMT91_00230, BON75_04205, BvCmsHHP019_05067, BvCmsSINP011_02211, D9H68_16155, D9J11_19520, E2127_01880, E2128_04080, E2134_03530, FORC82_1677, G9P50_07470, ...Gene: psuK, psuK_1, psuK_2, A8C65_16945, BMT91_00230, BON75_04205, BvCmsHHP019_05067, BvCmsSINP011_02211, D9H68_16155, D9J11_19520, E2127_01880, E2128_04080, E2134_03530, FORC82_1677, G9P50_07470, GQE64_02140, GQM28_02110, HVV70_14180, HVX33_21995, HVZ33_08660, NCTC11022_02147, NCTC13216_04879, NCTC9706_04998, SAMEA3752557_00486, WP4S18E08_16210 Production host: Escherichia coli B (bacteria) / References: UniProt: A0A1V3W5E1, pseudouridine kinase #2: Chemical | ChemComp-K / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.7 Å3/Da / Density % sol: 66.77 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.2M magnesium formate, 20% PEG 3350, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 11, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 104841 / % possible obs: 99.7 % / Redundancy: 5.4 % / Biso Wilson estimate: 49.5724471261 Å2 / CC1/2: 0.99 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.15→2.23 Å / Num. unique obs: 10500 / CC1/2: 0.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KZH Resolution: 2.15054869646→33.2888937491 Å / SU ML: 0.507065525363 / Cross valid method: FREE R-VALUE / σ(F): 1.95834498789 / Phase error: 41.2002494246
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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 mean: 85.9681233502 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15054869646→33.2888937491 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 61.0291501445 Å / Origin y: -1.80495814318 Å / Origin z: 14.4077919991 Å
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Refinement TLS group | Selection details: all |