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- PDB-6x70: Rev1-DNA Binary Complex -

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Basic information

Entry
Database: PDB / ID: 6x70
TitleRev1-DNA Binary Complex
Components
  • DNA (5'-D(*CP*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3')
  • DNA (5'-D(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*G)-3')
  • DNA repair protein REV1
KeywordsREPLICATION/DNA / DNA polymerase / REPLICATION / REPLICATION-DNA complex
Function / homology
Function and homology information


deoxycytidyl transferase activity / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / error-free translesion synthesis / error-prone translesion synthesis / replication fork / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / damaged DNA binding ...deoxycytidyl transferase activity / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / error-free translesion synthesis / error-prone translesion synthesis / replication fork / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / damaged DNA binding / DNA-directed DNA polymerase activity / chromatin / mitochondrion / metal ion binding / nucleus / cytoplasm
Similarity search - Function
DNA repair protein Rev1 / : / DNA polymerase-iota, thumb domain / BRCT domain / 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 repair protein Rev1 / : / DNA polymerase-iota, thumb domain / BRCT domain / 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. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Dna Ligase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA repair protein REV1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsWeaver, T.M. / Freudenthal, B.D.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Visualizing Rev1 catalyze protein-template DNA synthesis.
Authors: Weaver, T.M. / Cortez, L.M. / Khoang, T.H. / Washington, M.T. / Agarwal, P.K. / Freudenthal, B.D.
History
DepositionMay 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 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
P: DNA (5'-D(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*G)-3')
T: DNA (5'-D(*CP*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3')
A: DNA repair protein REV1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1974
Polymers59,1733
Non-polymers241
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-51 kcal/mol
Surface area23730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.212, 73.916, 117.617
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: DNA chain DNA (5'-D(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*G)-3')


Mass: 3814.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*CP*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3')


Mass: 5037.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein DNA repair protein REV1 / Reversionless protein 1


Mass: 50320.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: REV1, YOR346W, O6339 / Production host: Escherichia coli (E. coli)
References: UniProt: P12689, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 15-23% PEG3350 and 200 mM ammonium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Apr 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→25 Å / Num. obs: 60116 / % possible obs: 99.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 21.69 Å2 / Rrim(I) all: 0.147 / Net I/σ(I): 10.3
Reflection shellResolution: 2.05→2.4069 Å / Redundancy: 2.9 % / Num. unique obs: 24230 / CC1/2: 0.644 / Rrim(I) all: 0.473 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WM1

5wm1


Resolution: 2.05→22.49 Å / SU ML: 0.2642 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.1073
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2614 3562 5.93 %
Rwork0.2099 56554 -
obs0.213 60116 91.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.15 Å2
Refinement stepCycle: LAST / Resolution: 2.05→22.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3455 572 1 463 4491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824209
X-RAY DIFFRACTIONf_angle_d0.95175818
X-RAY DIFFRACTIONf_chiral_restr0.055654
X-RAY DIFFRACTIONf_plane_restr0.0059651
X-RAY DIFFRACTIONf_dihedral_angle_d21.04481614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.27451490.26922286X-RAY DIFFRACTION91.34
2.08-2.10.32811420.25142384X-RAY DIFFRACTION96.38
2.1-2.140.28531490.25312419X-RAY DIFFRACTION96.61
2.14-2.170.31231560.25632374X-RAY DIFFRACTION96.56
2.17-2.210.36051510.24062387X-RAY DIFFRACTION96.14
2.21-2.240.32941440.23192385X-RAY DIFFRACTION95.87
2.24-2.280.26281470.24562365X-RAY DIFFRACTION95.59
2.28-2.330.26511500.22712368X-RAY DIFFRACTION95.31
2.33-2.380.30991530.23422391X-RAY DIFFRACTION95.17
2.38-2.430.29961470.24272291X-RAY DIFFRACTION94.28
2.43-2.480.28251570.24972375X-RAY DIFFRACTION93.85
2.48-2.550.31831450.24622291X-RAY DIFFRACTION92.87
2.55-2.610.32451440.2452297X-RAY DIFFRACTION92.67
2.61-2.690.30381450.24712246X-RAY DIFFRACTION91.36
2.69-2.780.36851330.25772192X-RAY DIFFRACTION88.1
2.78-2.880.32731260.28542092X-RAY DIFFRACTION84.3
2.88-2.990.43951370.33112095X-RAY DIFFRACTION84.64
2.99-3.130.29781430.25122181X-RAY DIFFRACTION87.6
3.13-3.290.26721360.20562262X-RAY DIFFRACTION90.56
3.29-3.50.2531360.18532217X-RAY DIFFRACTION89.2
3.5-3.770.22631350.16542149X-RAY DIFFRACTION87.11
3.77-4.140.17851350.16482152X-RAY DIFFRACTION86.11
4.14-4.740.19081310.15992077X-RAY DIFFRACTION83.57
4.74-5.950.21281290.16642097X-RAY DIFFRACTION84.93
5.95-22.490.16391420.15132181X-RAY DIFFRACTION87.66

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