+Open data
-Basic information
Entry | Database: PDB / ID: 6k5z | ||||||
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Title | Structure of uridylyltransferase | ||||||
Components | Galactose-1-phosphate uridylyltransferase | ||||||
Keywords | TRANSFERASE / half-barrel | ||||||
Function / homology | Function and homology information UDP-glucose-hexose-1-phosphate uridylyltransferase / UDP-glucose:hexose-1-phosphate uridylyltransferase activity / galactose catabolic process via UDP-galactose / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrobaculum aerophilum str. IM2 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.33 Å | ||||||
Authors | Sakuraba, H. / Ohshida, T. / Yoneda, K. / Ohshima, T. | ||||||
Citation | Journal: Proteins / Year: 2020 Title: Unique active site formation in a novel galactose 1-phosphate uridylyltransferase from the hyperthermophilic archaeon Pyrobaculum aerophilum. Authors: Ohshida, T. / Hayashi, J. / Yoneda, K. / Ohshima, T. / Sakuraba, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k5z.cif.gz | 138.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k5z.ent.gz | 107.7 KB | Display | PDB format |
PDBx/mmJSON format | 6k5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k5z_validation.pdf.gz | 451.7 KB | Display | wwPDB validaton report |
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Full document | 6k5z_full_validation.pdf.gz | 458.5 KB | Display | |
Data in XML | 6k5z_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 6k5z_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/6k5z ftp://data.pdbj.org/pub/pdb/validation_reports/k5/6k5z | HTTPS FTP |
-Related structure data
Related structure data | 6k9zC 1gupS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 36163.641 Da / Num. of mol.: 2 / Mutation: F262I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrobaculum aerophilum str. IM2 (archaea) Strain: IM2 / Gene: PAE1184 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZXN7 #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: 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: 2.35 Å3/Da / Density % sol: 47.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 8000, Mg acetate, MES buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.33→50 Å / Num. obs: 28397 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.032 / Rrim(I) all: 0.087 / Χ2: 1.64 / Net I/σ(I): 11.6 / Num. measured all: 209601 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1gup Resolution: 2.33→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.583 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.405 / ESU R Free: 0.263 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 152.4 Å2 / Biso mean: 53.169 Å2 / Biso min: 18.42 Å2
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Refinement step | Cycle: final / Resolution: 2.33→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.329→2.389 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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