+Open data
-Basic information
Entry | Database: PDB / ID: 7tl4 | ||||||||||||
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Title | Crystal Structure of Yeast p58C Multi-Tyrosine Mutant 6YF | ||||||||||||
Components | DNA primase large subunit | ||||||||||||
Keywords | REPLICATION / 4Fe-4S cluster / DNA binding | ||||||||||||
Function / homology | IRON/SULFUR CLUSTER / : Function and homology information | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.805 Å | ||||||||||||
Authors | Blee, A.M. / Salay, L.E. / Chazin, W.J. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Biochemistry / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tl4.cif.gz | 94.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tl4.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 7tl4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tl4_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7tl4_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7tl4_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 7tl4_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/7tl4 ftp://data.pdbj.org/pub/pdb/validation_reports/tl/7tl4 | HTTPS FTP |
-Related structure data
Related structure data | 7tl2C 7tl3C 6dtzS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23267.309 Da / Num. of mol.: 1 / Fragment: C-terminal domain / Mutation: Y352F, Y353F, Y395F, Y397F, Y412F, Y431F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PACBIOSEQ_LOCUS3693 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7I9C0U2 |
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#2: Chemical | ChemComp-SF4 / |
#3: Chemical | ChemComp-MPD / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.51 % |
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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: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 6, 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: 1.8→30 Å / Num. obs: 16970 / % possible obs: 97 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.041 / Rrim(I) all: 0.095 / Χ2: 1.019 / Net I/σ(I): 13.7 / Num. measured all: 90999 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6DTZ Resolution: 1.805→29.606 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.95 / 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: 97.97 Å2 / Biso mean: 40.6517 Å2 / Biso min: 22.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.805→29.606 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: -15.7984 Å / Origin y: 1.2239 Å / Origin z: -14.6574 Å
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Refinement TLS group |
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