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- PDB-3rbe: Dpo4 extension ternary complex with 3'-terminal primer t base opp... -

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Basic information

Entry
Database: PDB / ID: 3rbe
TitleDpo4 extension ternary complex with 3'-terminal primer t base opposite the 3-methylcytosine (m3c) lesion
Components
  • DNA (5'-D(*C*CP*TP*AP*AP*CP*(ME6)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3')
  • DNA (5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DT))-3')
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / DNA DAMAGE / DNA REPAIR / DNA REPLICATION / DNA-BINDING / DNA-DIRECTED DNA POLYMERASE / MAGNESIUM / METAL-BINDING / MUTATOR PROTEIN / NUCLEOTIDYLTRANSFERASE / TRANSFERASE / TRANSFERASE-DNA COMPLEX / Lesion bypass / DNA polymerase / Y-family polymerase / dNTP-binding / 3-methylcytosine
Function / homology
Function and homology information


error-prone translesion synthesis / DNA-templated DNA replication / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / magnesium ion binding / cytoplasm
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 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
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRechkoblit, O. / Patel, D.J.
CitationJournal: Structure / Year: 2011
Title: Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions.
Authors: Rechkoblit, O. / Delaney, J.C. / Essigmann, J.M. / Patel, D.J.
History
DepositionMar 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Sep 13, 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_dif / 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.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_ref_seq_dif.details / _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 IV
D: DNA (5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DT))-3')
E: DNA (5'-D(*C*CP*TP*AP*AP*CP*(ME6)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3')
B: DNA polymerase IV
H: DNA (5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DT))-3')
J: DNA (5'-D(*C*CP*TP*AP*AP*CP*(ME6)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,15514
Polymers97,9006
Non-polymers1,2558
Water66737
1
A: DNA polymerase IV
D: DNA (5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DT))-3')
E: DNA (5'-D(*C*CP*TP*AP*AP*CP*(ME6)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5777
Polymers48,9503
Non-polymers6274
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-61 kcal/mol
Surface area20450 Å2
MethodPISA
2
B: DNA polymerase IV
H: DNA (5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DT))-3')
J: DNA (5'-D(*C*CP*TP*AP*AP*CP*(ME6)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5777
Polymers48,9503
Non-polymers6274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-53 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.904, 109.860, 101.291
Angle α, β, γ (deg.)90.00, 100.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase IV / Pol IV


Mass: 38945.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: dbh, dpo4, SSO2448 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL Codon plus / References: UniProt: Q97W02, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules DHEJ

#2: DNA chain DNA (5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DT))-3')


Mass: 4061.656 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic
#3: DNA chain DNA (5'-D(*C*CP*TP*AP*AP*CP*(ME6)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3')


Mass: 5942.896 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic

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Non-polymers , 3 types, 45 molecules

#4: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES, pH 7.0, 100 mM calcium acetate and 10% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 17, 2006
RadiationMonochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 27028 / % possible obs: 96 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 / Redundancy: 4.1 %
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.9 % / % possible all: 96

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RAQ

3raq


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.902 / SU B: 37.771 / SU ML: 0.345 / Cross valid method: THROUGHOUT / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26553 1340 5 %RANDOM
Rwork0.22616 ---
all0.22823 26598 --
obs0.22823 25336 95.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 86.266 Å2
Baniso -1Baniso -2Baniso -3
1--2.3 Å20 Å24.67 Å2
2---1.61 Å20 Å2
3---5.69 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5480 1052 68 37 6637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226814
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.522.1989377
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3625680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23723.636242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.367151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3241548
X-RAY DIFFRACTIONr_chiral_restr0.1130.21074
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214596
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4881.53409
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.73925518
X-RAY DIFFRACTIONr_scbond_it1.12333405
X-RAY DIFFRACTIONr_scangle_it1.9364.53859
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 89 -
Rwork0.382 1903 -
obs--99.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.3277-0.94-0.39632.4360.40851.4943-0.102-0.2983-0.00630.16330.16840.01360.0210.11-0.06640.024-0.0004-0.0090.07080.02280.135312.6971.47182.5656
23.66170.6447-0.73251.7932-2.22914.88260.0483-0.6154-0.64870.5544-0.1816-0.0951-0.37650.13910.13330.6971-0.1879-0.02090.70060.07250.3284-7.23556.769439.5619
32.7684-1.193-0.19431.92270.40921.63-0.5193-1.1908-0.19060.86350.4731-0.2658-0.02170.53350.04620.47260.1014-0.07460.68380.05950.356622.0577-6.370512.6143
414.4147-0.499-4.13795.8917-1.57845.1139-0.593-1.6542-2.46520.8564-0.4664-0.17830.33610.4911.05940.6746-0.11710.00861.04980.31440.74-1.309447.27343.5474
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 341
2X-RAY DIFFRACTION2B1001 - 1341
3X-RAY DIFFRACTION3D802 - 814
4X-RAY DIFFRACTION3E901 - 919
5X-RAY DIFFRACTION3A414
6X-RAY DIFFRACTION4H1806 - 1814
7X-RAY DIFFRACTION4J1905 - 1914
8X-RAY DIFFRACTION4B1414

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