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- PDB-5vtp: X-ray diffraction data of DNA Polymerase Eta (RAD30) of Saccharom... -

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Basic information

Entry
Database: PDB / ID: 5vtp
TitleX-ray diffraction data of DNA Polymerase Eta (RAD30) of Saccharomyces cerevisiae with a single magnesium bound in absence of DNA and incoming dNTP
ComponentsDNA polymerase eta
KeywordsTRANSFERASE / Rad30 / DNA Polymerase Eta / DNA Transferase / Catalytic Domain
Function / homology
Function and homology information


Translesion Synthesis by POLH / Termination of translesion DNA synthesis / mitotic sister chromatid cohesion / error-free translesion synthesis / error-prone translesion synthesis / replication fork / chromosome segregation / response to radiation / site of double-strand break / DNA replication ...Translesion Synthesis by POLH / Termination of translesion DNA synthesis / mitotic sister chromatid cohesion / error-free translesion synthesis / error-prone translesion synthesis / replication fork / chromosome segregation / response to radiation / site of double-strand break / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / mitochondrion / nucleus / metal ion binding
Similarity search - Function
DNA polymerase eta, ubiquitin-binding zinc finger / : / Zinc finger UBZ3-type profile. / 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 eta, ubiquitin-binding zinc finger / : / Zinc finger UBZ3-type profile. / 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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPowers, K.T. / Washington, M.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM081433 United States
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: The C-terminal region of translesion synthesis DNA polymerase eta is partially unstructured and has high conformational flexibility.
Authors: Powers, K.T. / Elcock, A.H. / Washington, M.T.
History
DepositionMay 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase eta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8563
Polymers60,8081
Non-polymers492
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DNA polymerase eta
hetero molecules

A: DNA polymerase eta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,7136
Polymers121,6152
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area1250 Å2
ΔGint-39 kcal/mol
Surface area46080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.681, 130.681, 93.908
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein DNA polymerase eta / Radiation-sensitive protein 30


Mass: 60807.742 Da / Num. of mol.: 1 / Fragment: Catalytic domain fragment (UNP residues 1-528)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RAD30, DBH1, YDR419W / Plasmid: pET-11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q04049, DNA-directed DNA polymerase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.99 Å3/Da / Density % sol: 69.16 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% v/v Glycerin (Additive), 14.4% w/v PEG 8000 (Precipitant), 0.08 M NaCac 6.5 pH (Buffer), 0.16 M Ca(OAc)2 (Salt)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 18, 2017
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→56.587 Å / Num. all: 23171 / Num. obs: 23171 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 69.23 Å2 / Rpim(I) all: 0.032 / Rrim(I) all: 0.105 / Rsym value: 0.096 / Net I/av σ(I): 6 / Net I/σ(I): 18.8 / Num. measured all: 245725
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.8-2.9510.71.0240.80.3431.1261.024100
2.95-3.1310.50.6071.30.2050.6680.607100
3.13-3.35100.3182.30.1110.3520.318100
3.35-3.6110.10.1694.40.0580.1870.169100
3.61-3.9610.90.1116.60.0360.120.111100
3.96-4.4311.10.0739.60.0240.0790.073100
4.43-5.1111.10.0611.20.0190.0650.06100
5.11-6.2610.90.05910.90.020.0650.059100
6.26-8.8510.70.04911.30.0160.0530.049100
8.85-56.5879.80.04711.40.0160.0510.04799.3

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Blu-Icedata collection
XDSNovember 1, 2016data reduction
SCALA3.3.22data scaling
PHASERphasing
Coot0.8.6.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JIH

1jih


Resolution: 2.8→43.37 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 27.05
RfactorNum. reflection% reflection
Rfree0.249 2264 5.12 %
Rwork0.2208 --
obs0.2223 23171 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 292.33 Å2 / Biso mean: 79.644 Å2 / Biso min: 35.85 Å2
Refinement stepCycle: final / Resolution: 2.8→43.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3957 0 2 23 3982
Biso mean--94.17 58.89 -
Num. residues----510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034040
X-RAY DIFFRACTIONf_angle_d0.6195470
X-RAY DIFFRACTIONf_chiral_restr0.041622
X-RAY DIFFRACTIONf_plane_restr0.004698
X-RAY DIFFRACTIONf_dihedral_angle_d13.1392434
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8-2.86090.41521320.358326352767
2.8609-2.92740.34061720.31826122784
2.9274-3.00060.28561040.301126292733
3.0006-3.08170.3081260.285426252751
3.0817-3.17240.35191280.295226722800
3.1724-3.27480.3031500.272826132763
3.2748-3.39180.31561660.266125432709
3.3918-3.52750.26291560.235926262782
3.5275-3.6880.23371280.223826162744
3.688-3.88230.25371620.209626132775
3.8823-4.12540.2031680.194826012769
4.1254-4.44360.22121820.178725822764
4.4436-4.89020.18891420.165526172759
4.8902-5.59660.2271300.183526202750
5.5966-7.04620.25691140.223726542768
7.0462-43.37470.24051040.218226552759

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