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- PDB-2xgp: Yeast DNA polymerase eta in complex with C8-2-acetylaminofluorene... -

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Basic information

Entry
Database: PDB / ID: 2xgp
TitleYeast DNA polymerase eta in complex with C8-2-acetylaminofluorene containing DNA
Components
  • 5'-D(*CP*8FG*CP*TP*CP*AP*TP*CP*CP*AP*C)-3'
  • 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'
  • DNA POLYMERASE ETA
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / TRANSLESION DNA SYNTHESIS / DNA-BINDING / DNA DAMAGE
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-directed DNA polymerase ...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-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA replication / mitochondrion / zinc ion binding / nucleus
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
DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsScheider, S. / Lammens, K. / Schorr, S. / Hopfner, K.P. / Carell, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Mechanism of Replication Blocking and Bypass of Y-Family Polymerase Eta by Bulky Acetylaminofluorene DNA Adducts.
Authors: Schorr, S. / Schneider, S. / Lammens, K. / Hopfner, K.P. / Carell, T.
History
DepositionJun 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 6, 2017Group: Advisory / Atomic model / Source and taxonomy
Category: atom_site / entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _entity_src_gen.pdbx_host_org_scientific_name
Revision 2.1Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA POLYMERASE ETA
B: DNA POLYMERASE ETA
P: 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'
Q: 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'
T: 5'-D(*CP*8FG*CP*TP*CP*AP*TP*CP*CP*AP*C)-3'
U: 5'-D(*CP*8FG*CP*TP*CP*AP*TP*CP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,36014
Polymers134,0406
Non-polymers3218
Water1,60389
1
B: DNA POLYMERASE ETA
Q: 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'
U: 5'-D(*CP*8FG*CP*TP*CP*AP*TP*CP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1807
Polymers67,0203
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-61.4 kcal/mol
Surface area26620 Å2
MethodPISA
2
A: DNA POLYMERASE ETA
P: 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'
T: 5'-D(*CP*8FG*CP*TP*CP*AP*TP*CP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1807
Polymers67,0203
Non-polymers1604
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-71.7 kcal/mol
Surface area26150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.440, 103.440, 292.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DNA POLYMERASE ETA / RADIATION-SENSITIVE PROTEIN 30


Mass: 60708.648 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-513
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PDEST007 / Production host: Escherichia coli / Strain (production host): ROSETTA / References: UniProt: Q04049, DNA-directed DNA polymerase
#2: DNA chain 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'


Mass: 2835.871 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*8FG*CP*TP*CP*AP*TP*CP*CP*AP*C)-3'


Mass: 3475.392 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1-513 WITH N-TERMINAL STREP-TAG

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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: 3.04 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growDetails: 4MG/ML, 11-14% PEG3350, 0.15-0.2M CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9129
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9129 Å / Relative weight: 1
ReflectionResolution: 2.7→49 Å / Num. obs: 44372 / % possible obs: 98.2 % / Observed criterion σ(I): 1.5 / Redundancy: 13.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 26.84
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 5.99 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JIH

2jih


Resolution: 2.7→48.76 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.866 / SU B: 11.857 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.834 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. OCCUPANCY OF DISORDERED ATOMS WAS SET TO ZERO DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27219 3592 8.1 %RANDOM
Rwork0.21972 ---
obs0.224 40624 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.494 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8116 824 8 89 9037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0229118
X-RAY DIFFRACTIONr_bond_other_d0.0010.026051
X-RAY DIFFRACTIONr_angle_refined_deg1.4422.08512489
X-RAY DIFFRACTIONr_angle_other_deg0.914314791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79451029
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86824.714350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.732151502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0741539
X-RAY DIFFRACTIONr_chiral_restr0.070.21394
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029492
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021702
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6131.55090
X-RAY DIFFRACTIONr_mcbond_other0.0821.52068
X-RAY DIFFRACTIONr_mcangle_it1.21728224
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.65434028
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8334.54260
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 262 -
Rwork0.301 2913 -
obs--100 %

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