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- PDB-6x76: Rev1 L325G Mn2+-facilitated Product Complex with second dCTP bound -

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Basic information

Entry
Database: PDB / ID: 6x76
TitleRev1 L325G Mn2+-facilitated Product Complex with second dCTP bound
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*GP*C)-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 / nucleus / metal ion binding / cytoplasm
Similarity search - Function
DNA repair protein Rev1 / : / DNA polymerase-iota, thumb domain / BRCT domain, a BRCA1 C-terminus domain / 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. ...DNA repair protein Rev1 / : / DNA polymerase-iota, thumb domain / BRCT domain, a BRCA1 C-terminus domain / 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 / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / : / 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: 2.53 Å
AuthorsWeaver, T.M. / Freudenthal, B.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
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*GP*C)-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)60,0938
Polymers59,4063
Non-polymers6875
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-68 kcal/mol
Surface area23190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.965, 73.626, 117.634
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

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DNA chain , 2 types, 2 molecules PT

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


Mass: 4103.655 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)

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Protein , 1 types, 1 molecules A

#3: Protein DNA repair protein REV1 / Reversionless protein 1


Mass: 50264.781 Da / Num. of mol.: 1 / Mutation: L325G
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

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Non-polymers , 3 types, 80 molecules

#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 15-23% PEG3350, 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: May 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.53→35.13 Å / Num. obs: 31942 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 42.45 Å2 / Rrim(I) all: 0.165 / Net I/σ(I): 7.8
Reflection shellResolution: 2.53→3.0697 Å / Num. unique obs: 12900 / CC1/2: 0.649

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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: 2.53→35.13 Å / SU ML: 0.3748 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6736
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2722 3186 9.97 %
Rwork0.2028 28756 -
obs0.2096 31942 92.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.13 Å2
Refinement stepCycle: LAST / Resolution: 2.53→35.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3464 591 32 75 4162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01024267
X-RAY DIFFRACTIONf_angle_d1.20555905
X-RAY DIFFRACTIONf_chiral_restr0.0646660
X-RAY DIFFRACTIONf_plane_restr0.0063655
X-RAY DIFFRACTIONf_dihedral_angle_d20.37771625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.570.2639680.2366613X-RAY DIFFRACTION45.77
2.57-2.610.3108960.2468866X-RAY DIFFRACTION62.88
2.61-2.650.30981080.29121016X-RAY DIFFRACTION75.84
2.65-2.70.34841330.29111171X-RAY DIFFRACTION85.73
2.7-2.750.38411320.2691229X-RAY DIFFRACTION92.15
2.75-2.80.34621450.25611285X-RAY DIFFRACTION94.89
2.8-2.860.37981430.26251334X-RAY DIFFRACTION96.22
2.86-2.920.34081370.25011310X-RAY DIFFRACTION97.38
2.92-2.990.37241510.24091310X-RAY DIFFRACTION97.99
2.99-3.060.33861490.2471339X-RAY DIFFRACTION97.89
3.06-3.140.34121480.25951321X-RAY DIFFRACTION97.67
3.14-3.240.29191510.23061330X-RAY DIFFRACTION97.88
3.24-3.340.28331490.20041321X-RAY DIFFRACTION97.8
3.34-3.460.26731520.18791336X-RAY DIFFRACTION98.61
3.46-3.60.24311420.18271324X-RAY DIFFRACTION98.32
3.6-3.760.25291500.18141332X-RAY DIFFRACTION98.47
3.76-3.960.25071470.17981353X-RAY DIFFRACTION98.62
3.96-4.210.26331420.17671348X-RAY DIFFRACTION98.48
4.21-4.530.24951500.16481311X-RAY DIFFRACTION98.45
4.53-4.990.25371530.17311338X-RAY DIFFRACTION98.22
4.99-5.710.23291530.19151328X-RAY DIFFRACTION98.47
5.71-7.180.24541510.21531333X-RAY DIFFRACTION98.47
7.18-35.130.21411360.18541308X-RAY DIFFRACTION95.69

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