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Basic information

Entry
Database: PDB / ID: 3khg
TitleDpo4 extension ternary complex with misinserted A opposite the 2-aminofluorene-guanine [AF]G lesion
Components
  • 5'-D(*C*CP*TP*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'
  • 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3'
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / Lesion bypass / DNA polymerase / Y-family polymerase / 2-aminofluorene / semi-targeted mutagenesis / 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


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, 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
2-AMINOFLUORENE / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsRechkoblit, O. / Malinina, L. / Patel, D.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4.
Authors: Rechkoblit, O. / Kolbanovskiy, A. / Malinina, L. / Geacintov, N.E. / Broyde, S. / Patel, D.J.
History
DepositionOct 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 13, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq / 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_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_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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase IV
B: DNA polymerase IV
D: 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3'
E: 5'-D(*C*CP*TP*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'
H: 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3'
J: 5'-D(*C*CP*TP*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,24517
Polymers97,3906
Non-polymers1,85611
Water90150
1
A: DNA polymerase IV
D: 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3'
E: 5'-D(*C*CP*TP*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7429
Polymers48,6953
Non-polymers1,0476
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-28.8 kcal/mol
Surface area20990 Å2
MethodPISA
2
B: DNA polymerase IV
H: 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3'
J: 5'-D(*C*CP*TP*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5038
Polymers48,6953
Non-polymers8095
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-26.1 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.811, 110.948, 100.772
Angle α, β, γ (deg.)90.00, 101.38, 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 P2 (archaea) / Strain: P2 / DSM 1617 / JCM 11322 / Gene: dbh, dpo4, SSO2448 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL(STRATAGENE) / References: UniProt: Q97W02, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules DHEJ

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


Mass: 4070.668 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: DNA primer strand (Dideoxy-terminated at the 3'-end)
#3: DNA chain 5'-D(*C*CP*TP*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'


Mass: 5678.703 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA [AF]G-modified template strand

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Non-polymers , 5 types, 61 molecules

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


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Chemical ChemComp-AF / 2-AMINOFLUORENE / 2-Aminofluorene


Mass: 181.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11N
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsIn chains E and J, the 19-mer sequence of the DNA oligo is 5'-C T A A C [AF]G C T A C C A T C C A A ...In chains E and J, the 19-mer sequence of the DNA oligo is 5'-C T A A C [AF]G C T A C C A T C C A A C C-3', where [AF]G denotes a covalent modification by AF on the G base 906 in chain E and the G base 1906 in chain J: D(*C*TP*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP* CP)-3'

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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: 58.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES pH 7.0, 100 mM Calcium acetate, 10% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2Calcium acetate11
3PEG 400011
4HEPES12
5Calcium acetate12
6PEG 400012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.96→20 Å / Num. obs: 23080 / % possible obs: 96.2 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 11.4
Reflection shellResolution: 2.96→3.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2246 / % possible all: 94.3

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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 2ASD

2asd


Resolution: 2.96→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.888 / SU B: 41.996 / SU ML: 0.367 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.477 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28166 1224 5.4 %RANDOM
Rwork0.20479 ---
obs0.20897 21625 96.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.693 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å20 Å23.85 Å2
2---0.53 Å20 Å2
3---4.07 Å2
Refinement stepCycle: LAST / Resolution: 2.96→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5480 999 111 50 6640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226809
X-RAY DIFFRACTIONr_bond_other_d0.0010.024518
X-RAY DIFFRACTIONr_angle_refined_deg1.6042.1959352
X-RAY DIFFRACTIONr_angle_other_deg0.925311052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3725680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91623.636242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.866151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1571548
X-RAY DIFFRACTIONr_chiral_restr0.110.21062
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026582
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021226
X-RAY DIFFRACTIONr_mcbond_it0.6741.53419
X-RAY DIFFRACTIONr_mcbond_other0.0541.51380
X-RAY DIFFRACTIONr_mcangle_it0.8325522
X-RAY DIFFRACTIONr_scbond_it1.23733390
X-RAY DIFFRACTIONr_scangle_it2.1874.53830
LS refinement shellResolution: 2.96→3.035 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.498 81 -
Rwork0.331 1508 -
obs--94.02 %
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)
12.3652-0.5991-0.02231.95250.46571.5759-0.0102-0.2201-0.0180.15590.09250.1719-0.1580.0862-0.08230.1891-0.01180.02010.23730.02370.275712.9331.76262.5266
23.58450.0732-1.27941.2447-0.69223.9640.0445-0.4699-0.25220.405-0.01640.0247-0.27120.0205-0.02820.2731-0.09640.00290.2565-0.00060.0353-7.0557.864239.2497
31.79090.0303-0.99463.03260.90992.9235-0.1106-0.4955-0.22730.65880.22210.06750.17160.7197-0.11150.38070.0906-0.15560.56560.08440.269822.0488-6.307612.4162
49.4056-2.8285-9.57193.26424.31710.599-0.2798-0.4421-1.03111.1413-0.2342-0.14020.68690.41330.5140.5376-0.0363-0.20960.88310.2850.2528-2.684348.124342.2507
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 341
2X-RAY DIFFRACTION2B1001 - 1341
3X-RAY DIFFRACTION3D802 - 813
4X-RAY DIFFRACTION3E901 - 919
5X-RAY DIFFRACTION3A414
6X-RAY DIFFRACTION3E926
7X-RAY DIFFRACTION4H1805 - 1813
8X-RAY DIFFRACTION4J1905 - 1913
9X-RAY DIFFRACTION4B1414
10X-RAY DIFFRACTION4J1926

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