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- PDB-3rb4: Dpo4 extension ternary complex with 3'-terminal primer G base opp... -

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Basic information

Entry
Database: PDB / ID: 3rb4
TitleDpo4 extension ternary complex with 3'-terminal primer G 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*(DDG))-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: 2.805 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 28, 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*(DDG))-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*(DDG))-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)99,20514
Polymers97,9506
Non-polymers1,2558
Water1,20767
1
A: DNA polymerase IV
D: DNA (5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(DDG))-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)49,6027
Polymers48,9753
Non-polymers6274
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-59 kcal/mol
Surface area20670 Å2
MethodPISA
2
B: DNA polymerase IV
H: DNA (5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(DDG))-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)49,6027
Polymers48,9753
Non-polymers6274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-61 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.267, 109.995, 101.535
Angle α, β, γ (deg.)90.00, 101.35, 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*(DDG))-3')


Mass: 4086.668 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, 75 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.: 67 / 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: 2.98 Å3/Da / Density % sol: 58.69 %
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2007
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: 27360 / % possible obs: 98.6 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 2.2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.073
Reflection shellResolution: 2.8→2.89 Å / Num. unique all: 2270 / % possible all: 91.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RAQ

3raq


Resolution: 2.805→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9 / SU B: 28.526 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25644 1367 5 %RANDOM
Rwork0.20504 ---
all0.20765 26684 --
obs0.20765 25974 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.817 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å20 Å22.82 Å2
2---1.11 Å20 Å2
3---4.42 Å2
Refinement stepCycle: LAST / Resolution: 2.805→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5480 1085 68 67 6700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226852
X-RAY DIFFRACTIONr_angle_refined_deg1.4542.2029431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.135680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60223.636242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.054151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5741548
X-RAY DIFFRACTIONr_chiral_restr0.130.21079
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214608
X-RAY DIFFRACTIONr_mcbond_it0.7821.53411
X-RAY DIFFRACTIONr_mcangle_it0.86125518
X-RAY DIFFRACTIONr_scbond_it1.37733441
X-RAY DIFFRACTIONr_scangle_it2.3854.53913
LS refinement shellResolution: 2.805→2.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 71 -
Rwork0.257 1426 -
obs--74.81 %
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)
13.5304-0.9741-0.12452.38650.13091.1628-0.1398-0.2738-0.04250.16230.22380.01310.00080.1046-0.0840.05550.00950.0040.04330.01340.10412.70311.50862.5884
24.31040.6698-1.23251.0856-1.82916.3416-0.0319-0.6744-0.65180.2623-0.1961-0.2525-0.1871-0.06010.22790.6686-0.15260.02960.71640.07380.3497-7.46956.850539.3939
32.4274-0.7899-1.43432.94820.56642.0695-0.3053-0.9412-0.18160.62530.3696-0.09840.16830.6449-0.06430.20760.1024-0.07460.38350.07980.14422.147-6.49412.5371
49.12020.3645-2.24610.27550.6072.6636-0.4257-1.1382-1.79810.4237-0.2953-0.0280.9378-0.16260.72091.2321-0.1646-0.03741.25040.43141.1265-0.34446.63843.8064
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 - 1915
8X-RAY DIFFRACTION4B1414

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