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- PDB-2rdj: Snapshots of a Y-family DNA polymerase in replication: Dpo4 in ap... -

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Basic information

Entry
Database: PDB / ID: 2rdj
TitleSnapshots of a Y-family DNA polymerase in replication: Dpo4 in apo and binary/ternary complex forms
Components
  • DNA (5'-D(*DGP*DGP*DGP*DAP*DCP*DCP*DCP*DTP*DTP*DCP*DGP*DAP*DAP*DT)-3')
  • DNA (5'-D(P*DTP*DAP*DTP*DTP*DCP*DGP*DAP*DAP*DGP*DGP*DGP*DTP*DCP*DCP*DC)-3')
  • DNA (5'-D(P*DTP*DTP*DAP*DTP*DTP*DCP*DGP*DAP*DAP*DGP*DGP*DGP*DTP*DCP*DCP*DC)-3')
  • DNA polymerase IV
KeywordsTransferase/DNA / DNA polymerase / DNA-enzyme complex / Y-family / DNA damage / DNA repair / DNA replication / DNA-binding / DNA-directed DNA polymerase / Magnesium / Metal-binding / Mutator protein / Nucleotidyltransferase / Transferase / Transferase-DNA COMPLEX
Function / homology
Function and homology information


SOS response / error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytosol
Similarity search - Function
DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / 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 type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / 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
THYMIDINE-5'-PHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsWong, J.H.Y. / Ling, H.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Snapshots of a Y-family DNA polymerase in replication: substrate-induced conformational transitions and implications for fidelity of Dpo4.
Authors: Wong, J.H. / Fiala, K.A. / Suo, Z. / Ling, H.
History
DepositionSep 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: refine_ls_shell / software / Item: _refine_ls_shell.percent_reflns_R_free
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.pdbx_dist_value / _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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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
C: DNA (5'-D(*DGP*DGP*DGP*DAP*DCP*DCP*DCP*DTP*DTP*DCP*DGP*DAP*DAP*DT)-3')
D: DNA (5'-D(P*DTP*DTP*DAP*DTP*DTP*DCP*DGP*DAP*DAP*DGP*DGP*DGP*DTP*DCP*DCP*DC)-3')
E: DNA (5'-D(*DGP*DGP*DGP*DAP*DCP*DCP*DCP*DTP*DTP*DCP*DGP*DAP*DAP*DT)-3')
F: DNA (5'-D(P*DTP*DAP*DTP*DTP*DCP*DGP*DAP*DAP*DGP*DGP*DGP*DTP*DCP*DCP*DC)-3')
A: DNA polymerase IV
B: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,12612
Polymers98,5526
Non-polymers5756
Water5,495305
1
C: DNA (5'-D(*DGP*DGP*DGP*DAP*DCP*DCP*DCP*DTP*DTP*DCP*DGP*DAP*DAP*DT)-3')
D: DNA (5'-D(P*DTP*DTP*DAP*DTP*DTP*DCP*DGP*DAP*DAP*DGP*DGP*DGP*DTP*DCP*DCP*DC)-3')
A: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9227
Polymers49,4283
Non-polymers4944
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-65 kcal/mol
Surface area20110 Å2
MethodPISA
2
E: DNA (5'-D(*DGP*DGP*DGP*DAP*DCP*DCP*DCP*DTP*DTP*DCP*DGP*DAP*DAP*DT)-3')
F: DNA (5'-D(P*DTP*DAP*DTP*DTP*DCP*DGP*DAP*DAP*DGP*DGP*DGP*DTP*DCP*DCP*DC)-3')
B: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2045
Polymers49,1243
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-58 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.993, 102.510, 106.109
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is chain A alone or chain B alone.

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Components

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DNA chain , 3 types, 4 molecules CEDF

#1: DNA chain DNA (5'-D(*DGP*DGP*DGP*DAP*DCP*DCP*DCP*DTP*DTP*DCP*DGP*DAP*DAP*DT)-3')


Mass: 4280.792 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA primer strand
#2: DNA chain DNA (5'-D(P*DTP*DTP*DAP*DTP*DTP*DCP*DGP*DAP*DAP*DGP*DGP*DGP*DTP*DCP*DCP*DC)-3')


Mass: 4889.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA template strand from polypeptide chain A
#3: DNA chain DNA (5'-D(P*DTP*DAP*DTP*DTP*DCP*DGP*DAP*DAP*DGP*DGP*DGP*DTP*DCP*DCP*DC)-3')


Mass: 4584.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA template strand from polypeptide chain B

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Protein , 1 types, 2 molecules AB

#4: Protein DNA polymerase IV / / Pol IV


Mass: 40257.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: dbh, dpo4 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97W02, DNA-directed DNA polymerase

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Non-polymers , 4 types, 311 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 294 K / pH: 7
Details: 10-15% PEG3350, 0.2M calcium acetate, 0.1M HEPES pH 7.0, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG335011
2calcium acetate11
3HEPES11
4glycerol11
5PEG335012
6calcium acetate12
7HEPES12
8glycerol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: Graded Multilayer (OSMIC) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 53280 / Num. obs: 51948 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.1
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.36 / Num. unique all: 2513 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
RefinementStarting model: PDB ENTRY 1JX4

1jx4


Resolution: 2.2→24.11 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.829 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2660 5.1 %RANDOM
Rwork0.21 ---
all0.221 51924 --
obs0.221 51924 100 %-
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 45.17 Å2
Baniso -1Baniso -2Baniso -3
1-2.55 Å20 Å20 Å2
2---1.66 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.2→24.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5486 1202 31 305 7024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226948
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5022.2139576
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5545680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.20223.636242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.631151126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4481548
X-RAY DIFFRACTIONr_chiral_restr0.0870.21093
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024637
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.22872
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24645
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2460
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1520.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6781.53553
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11525520
X-RAY DIFFRACTIONr_scbond_it1.74434237
X-RAY DIFFRACTIONr_scangle_it2.7564.54056
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.205→2.262 Å
RfactorNum. reflection% reflection
Rfree0.352 199 -
Rwork0.285 --
obs--100 %

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