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- PDB-3khh: Dpo4 extension ternary complex with a C base opposite the 2-amino... -

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Basic information

Entry
Database: PDB / ID: 3khh
TitleDpo4 extension ternary complex with a C base opposite the 2-aminofluorene-guanine [AF]G lesion
Components
  • 5'-D(*CP*CP*TP*A*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*(DOC))-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: 2.7 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: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_conn.ptnr2_label_seq_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
D: 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(DOC))-3'
E: 5'-D(*CP*CP*TP*A*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'
B: DNA polymerase IV
H: 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(DOC))-3'
J: 5'-D(*CP*CP*TP*A*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)98,95916
Polymers97,3416
Non-polymers1,61710
Water1,65792
1
A: DNA polymerase IV
D: 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(DOC))-3'
E: 5'-D(*CP*CP*TP*A*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)49,4798
Polymers48,6713
Non-polymers8095
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-24.9 kcal/mol
Surface area21140 Å2
MethodPISA
2
B: DNA polymerase IV
H: 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(DOC))-3'
J: 5'-D(*CP*CP*TP*A*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)49,4798
Polymers48,6713
Non-polymers8095
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-31.6 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.746, 98.799, 98.638
Angle α, β, γ (deg.)90.00, 99.08, 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*(DOC))-3'


Mass: 4046.645 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: DNA primer strand (Dideoxy-terminated at the 3'-end)
#3: DNA chain 5'-D(*CP*CP*TP*A*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 , 4 types, 102 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-AF / 2-AMINOFLUORENE / 2-Aminofluorene


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


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsFor the 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 ...For the 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: 5'-D(*C*TP*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP* CP)-3' The A3 base should have a phosphate.

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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: 2.69 Å3/Da / Density % sol: 54.28 %
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-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 27915 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 13.6
Reflection shellResolution: 2.7→2.78 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2322 / % possible all: 97.9

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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: 2.7→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 28.049 / SU ML: 0.265 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25239 1415 5.1 %RANDOM
Rwork0.19151 ---
obs0.19465 26483 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.599 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å2-0.05 Å2
2--0.52 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5480 1194 96 92 6862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227009
X-RAY DIFFRACTIONr_angle_refined_deg1.3652.2229671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3555680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78923.636242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.198151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2161548
X-RAY DIFFRACTIONr_chiral_restr0.0960.21099
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214707
X-RAY DIFFRACTIONr_mcbond_it0.4961.53414
X-RAY DIFFRACTIONr_mcangle_it0.8525522
X-RAY DIFFRACTIONr_scbond_it1.17633595
X-RAY DIFFRACTIONr_scangle_it2.0324.54149
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 96 -
Rwork0.295 1778 -
obs--91.19 %
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)
11.76570.5466-0.07971.0681-0.28531.86410.03280.2463-0.136-0.1751-0.0853-0.18410.17750.0890.05250.10360.09120.03610.10970.00670.10313.04361.74171.2894
21.53670.66780.97421.37141.19822.93150.0239-0.0740.07150.01680.04070.0257-0.0205-0.0268-0.06450.09260.0282-0.01120.02060.00970.102632.27614.054942.7607
34.29992.1675-0.95444.24341.19943.9328-0.44050.2545-0.5506-0.54150.13810.030.203-0.25890.30240.2106-0.0337-0.08320.0865-0.08660.2692-1.4314-11.80750.3473
43.28570.1622-1.71892.60810.89137.3366-0.0236-0.375-0.2230.29280.22990.43040.6974-0.3131-0.20630.15540.02440.00720.2070.03980.270830.329412.1860.8031
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 DIFFRACTION3E904 - 919
5X-RAY DIFFRACTION3A414
6X-RAY DIFFRACTION4H1802 - 1814
7X-RAY DIFFRACTION4J1902 - 1919
8X-RAY DIFFRACTION4B1414

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