- PDB-4ruc: Crystal structure of Y-family DNA polymerase Dpo4 extending from ... -
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Basic information
Entry
Database: PDB / ID: 4ruc
Title
Crystal structure of Y-family DNA polymerase Dpo4 extending from a MeFapy-dG:dC pair
Components
(Nucleic acids ...Nucleic acid) x 2
DNA polymerase IV
Keywords
TRANSFERASE/DNA / Protein / DNA / DNA Damage / DNA-Directed DNA Polymerase / Adenosine triphosphate / Y-family polymerase / trans-lesion synthesis (TLS) / DNA Binding / MeFapy-dG lesion bypass / Primer Extension / 2 / 6-diamino-4-hydroxy N(5)-(methyl)-formamidopyrimidine (MeFapy-dG) lesion / TRANSFERASE-DNA complex
Function / homology
Function and homology information
SOS response / error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytosol Similarity search - Function
DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily ...DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Dna Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→69.88 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.914 / SU B: 16.157 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R Free: 0.388 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23561
581
4.9 %
RANDOM
Rwork
0.17162
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obs
0.17482
11228
98.62 %
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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