- PDB-5dqo: Crystal structure of Y347F mutant of human primase p58 iron-sulfu... -
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Basic information
Entry
Database: PDB / ID: 5dqo
Title
Crystal structure of Y347F mutant of human primase p58 iron-sulfur cluster domain
Components
DNA primase large subunit
Keywords
REPLICATION / Iron-Sulfur Cluster / DNA Priming
Function / homology
Function and homology information
positive regulation of DNA primase activity / DNA replication initiation / DNA/RNA hybrid binding / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / alpha DNA polymerase:primase complex / Polymerase switching / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Activation of the pre-replicative complex ...positive regulation of DNA primase activity / DNA replication initiation / DNA/RNA hybrid binding / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / alpha DNA polymerase:primase complex / Polymerase switching / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Activation of the pre-replicative complex / Polymerase switching on the C-strand of the telomere / primosome complex / DNA replication, synthesis of primer / DNA replication initiation / Defective pyroptosis / 4 iron, 4 sulfur cluster binding / DNA binding / nucleoplasm / metal ion binding Similarity search - Function
DNA primase, large subunit, eukaryotic / DNA primase large subunit, eukaryotic/archaeal / Eukaryotic and archaeal DNA primase, large subunit Similarity search - Domain/homology
Resolution: 2.3→44.14 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.743 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2749
2045
4.8 %
RANDOM
Rwork
0.25059
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obs
0.25174
40637
95.34 %
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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: 54.343 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.09 Å2
0 Å2
0 Å2
2-
-
1.09 Å2
0 Å2
3-
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-2.18 Å2
Refinement step
Cycle: LAST / Resolution: 2.3→44.14 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4863
0
32
14
4909
LS refinement shell
Resolution: 2.3→2.36 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.605
112
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Rwork
0.438
2170
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obs
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69.11 %
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