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Open data
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Basic information
Entry | Database: PDB / ID: 7tl3 | ||||||||||||
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Title | Crystal Structure of Yeast p58C Multi-Tyrosine Mutant 5YF431 | ||||||||||||
![]() | DNA primase large subunit | ||||||||||||
![]() | REPLICATION / 4Fe-4S cluster / DNA binding | ||||||||||||
Function / homology | IRON/SULFUR CLUSTER / : ![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Blee, A.M. / Salay, L.E. / Chazin, W.J. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Modification of the 4Fe-4S Cluster Charge Transport Pathway Alters RNA Synthesis by Yeast DNA Primase. Authors: Salay, L.E. / Blee, A.M. / Raza, M.K. / Gallagher, K.S. / Chen, H. / Dorfeuille, A.J. / Barton, J.K. / Chazin, W.J. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.9 KB | Display | ![]() |
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PDB format | ![]() | 67.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7tl2C ![]() 7tl4C ![]() 6dtzS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23283.309 Da / Num. of mol.: 1 / Fragment: C-terminal domain / Mutation: Y352F, Y353F, Y395F, Y397F, Y431F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PACBIOSEQ_LOCUS3693 / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-SF4 / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Protein drops contained 20 mM HEPES (pH 6.8), 75 mM NaCl, 2 mM DTT mixed with equal volume of 100 mM TRIS (pH 8.5) and 55-70% MPD. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 20, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.05→30.359 Å / Num. obs: 11722 / % possible obs: 96.8 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.078 / Rrim(I) all: 0.166 / Χ2: 1 / Net I/σ(I): 6.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6DTZ Resolution: 2.066→30.359 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.73 / Stereochemistry target values: ML
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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 max: 74.3 Å2 / Biso mean: 42.8526 Å2 / Biso min: 26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.066→30.359 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 4.3149 Å / Origin y: 24.6325 Å / Origin z: 14.3569 Å
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Refinement TLS group |
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