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- PDB-3raq: Dpo4 extension ternary complex with 3'-terminal primer C base opp... -

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Basic information

Entry
Database: PDB / ID: 3raq
TitleDpo4 extension ternary complex with 3'-terminal primer C base opposite the 1-methylguanine (MG1) lesion
Components
  • DNA (5'-D(*C*CP*TP*AP*AP*CP*(MG1)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*(DOC))-3')
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / PROTEIN-DNA COMPLEX / DNA DAMAGE / DNA REPAIR / DNA REPLICATION / DNA-BINDING / DNA-DIRECTED DNA POLYMERASE / NUCLEOTIDYLTRANSFERASE / TRANSFERASE / TRANSFERASE-DNA COMPLEX / Lesion bypass / DNA polymerase / Y-family polymerase / DNA binding / nucleotide (dNTP) binding / MAGNESIUM / METAL-BINDING / 1-methylguanine
Function / homology
Function and homology information


error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / 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: 2.25 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*(DOC))-3')
E: DNA (5'-D(*C*CP*TP*AP*AP*CP*(MG1)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*(DOC))-3')
J: DNA (5'-D(*C*CP*TP*AP*AP*CP*(MG1)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,67916
Polymers97,9486
Non-polymers1,73110
Water5,368298
1
A: DNA polymerase IV
D: DNA (5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(DOC))-3')
E: DNA (5'-D(*C*CP*TP*AP*AP*CP*(MG1)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8408
Polymers48,9743
Non-polymers8665
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-50 kcal/mol
Surface area19640 Å2
MethodPISA
2
B: DNA polymerase IV
H: DNA (5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(DOC))-3')
J: DNA (5'-D(*C*CP*TP*AP*AP*CP*(MG1)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8408
Polymers48,9743
Non-polymers8665
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-47 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.194, 62.077, 91.459
Angle α, β, γ (deg.)98.97, 103.82, 93.72
Int Tables number1
Space group name H-MP1

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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*(DOC))-3')


Mass: 4046.645 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic
#3: DNA chain DNA (5'-D(*C*CP*TP*AP*AP*CP*(MG1)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3')


Mass: 5981.912 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic

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Non-polymers , 4 types, 308 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: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.89 Å3/Da / Density % sol: 57.37 %
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-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2006
RadiationMonochromator: Kohzu HLD8-24 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. obs: 51859 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.107
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2 / Num. unique all: 3622 / % possible all: 96.8

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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 3GIJ

3gij


Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 12.384 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.269 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23505 2578 5.1 %RANDOM
Rwork0.19379 ---
obs0.19589 48438 98.27 %-
all-51859 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.889 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å20.06 Å2-0.32 Å2
2--0.05 Å2-0.05 Å2
3---1.84 Å2
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5480 1237 98 298 7113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227079
X-RAY DIFFRACTIONr_bond_other_d0.0010.024638
X-RAY DIFFRACTIONr_angle_refined_deg1.422.239770
X-RAY DIFFRACTIONr_angle_other_deg0.895311356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.25680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.67223.636242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6191548
X-RAY DIFFRACTIONr_chiral_restr0.1180.21109
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026677
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021232
X-RAY DIFFRACTIONr_mcbond_it0.5231.53415
X-RAY DIFFRACTIONr_mcbond_other0.0771.51376
X-RAY DIFFRACTIONr_mcangle_it0.88325518
X-RAY DIFFRACTIONr_scbond_it1.25933664
X-RAY DIFFRACTIONr_scangle_it2.044.54252
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 180 -
Rwork0.3 3544 -
obs--97.23 %
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)
11.35220.39090.11661.3675-0.18260.5555-0.04170.091-0.0822-0.08040.0197-0.0501-0.0007-0.04080.02190.05740.01690.0420.0386-0.02180.07121.57250.71132.2632
22.56980.10671.19780.8958-0.24111.7123-0.21730.00470.12050.01370.03370.0034-0.2446-0.04450.18360.10820.04640.00890.1191-0.02880.060125.305224.144940.965
32.03220.77850.52082.1626-0.21622.0911-0.2770.4778-0.1026-0.45940.1990.2486-0.055-0.19360.0780.1649-0.0263-0.00730.1929-0.0510.1341-7.8608-3.7993-10.1665
44.1170.97851.56642.62080.50142.2824-0.3864-0.43140.54720.047-0.0469-0.324-0.51020.28260.43330.2269-0.0194-0.09220.3297-0.02940.223635.409433.01451.5841
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 DIFFRACTION3E902 - 919
5X-RAY DIFFRACTION3A414
6X-RAY DIFFRACTION4H1802 - 1814
7X-RAY DIFFRACTION4J1903 - 1919
8X-RAY DIFFRACTION4B1414

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