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- PDB-5umv: Crystal structure of the BRCT domain of S. cerevisiae Rev1 -

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Basic information

Entry
Database: PDB / ID: 5umv
TitleCrystal structure of the BRCT domain of S. cerevisiae Rev1
ComponentsDNA repair protein REV1
KeywordsTRANSCRIPTION / Translesion DNA synthesis / DNA damage bypass / BRCT domain / PCNA / Rev1
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 / BRCT 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 ...DNA repair protein Rev1 / BRCT 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA repair protein REV1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLee, J. / Xu, C. / Thompson, J.R. / Botuyan, M.V. / Mer, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA132878 United States
CitationJournal: To Be Published
Title: Crystal structure of the BRCT domain of S. cerevisiae Rev1
Authors: Xu, C. / Cui, G. / Lee, J. / Thompson, J.R. / Botuyan, M.V. / Mer, G.
History
DepositionJan 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 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

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Assembly

Deposited unit
A: DNA repair protein REV1


Theoretical massNumber of molelcules
Total (without water)10,7041
Polymers10,7041
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.556, 33.556, 81.838
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 10703.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: REV1, YOR346W, O6339 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P12689, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Rev1 at 40 mg/mL in 20 mM Tris-HCl, pH 7.0, 50 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.749→33.56 Å / Num. obs: 8356 / % possible obs: 91.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 55.8

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Processing

Software
NameVersionClassification
PHENIXDEV_1106refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VX7

5vx7


Resolution: 1.75→33.56 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.18
RfactorNum. reflection% reflection
Rfree0.193 400 4.79 %
Rwork0.163 --
obs0.164 8356 91.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→33.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms733 0 0 95 828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002809
X-RAY DIFFRACTIONf_angle_d0.4961108
X-RAY DIFFRACTIONf_dihedral_angle_d10.615318
X-RAY DIFFRACTIONf_chiral_restr0.053127
X-RAY DIFFRACTIONf_plane_restr0.003135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7488-2.00190.22391130.19012164X-RAY DIFFRACTION75
2.0019-2.5220.20981560.18082887X-RAY DIFFRACTION100
2.522-33.56220.18071310.15282905X-RAY DIFFRACTION99

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