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Basic information

Entry
Database: PDB / ID: 2atl
TitleUnmodified Insertion Ternary Complex
Components
  • 5'-D(*CP*T*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'
  • 5'-D(*GP*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*(DDG))-3'
  • Dpo4 polymerase IV
Keywordstransferase/DNA / DNA polymerase / Y-family / lesion bypass / transferase-DNA COMPLEX
Function / homology
Function and homology information


SOS response / error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytosol
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'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRechkoblit, O. / Malinina, L. / Cheng, Y. / Kuryavyi, V. / Broyde, S. / Geacintov, N.E. / Patel, D.J.
CitationJournal: Plos Biol. / Year: 2006
Title: Stepwise Translocation of Dpo4 Polymerase during Error-Free Bypass of an oxoG Lesion
Authors: Rechkoblit, O. / Malinina, L. / Cheng, Y. / Kuryavyi, V. / Broyde, S. / Geacintov, N.E. / Patel, D.J.
History
DepositionAug 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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_conn_type / 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.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_conn_type.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
D: 5'-D(*GP*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*(DDG))-3'
E: 5'-D(*CP*T*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'
H: 5'-D(*GP*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*(DDG))-3'
J: 5'-D(*CP*T*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'
A: Dpo4 polymerase IV
B: Dpo4 polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,43716
Polymers101,1826
Non-polymers1,25510
Water2,648147
1
D: 5'-D(*GP*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*(DDG))-3'
E: 5'-D(*CP*T*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'
A: Dpo4 polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2188
Polymers50,5913
Non-polymers6275
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: 5'-D(*GP*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*(DDG))-3'
J: 5'-D(*CP*T*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'
B: Dpo4 polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2188
Polymers50,5913
Non-polymers6275
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.584, 101.758, 112.286
Angle α, β, γ (deg.)90.00, 94.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 4 molecules DHEJ

#1: DNA chain 5'-D(*GP*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*(DDG))-3'


Mass: 4086.668 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Primer Strand (dideoxy-terminated at 3'-end)
#2: DNA chain 5'-D(*CP*T*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: Template Strand

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Protein , 1 types, 2 molecules AB

#3: Protein Dpo4 polymerase IV / Pol IV


Mass: 40825.410 Da / Num. of mol.: 2 / Fragment: Dpo4 polymerase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL (Stratagene) / References: UniProt: Q97W02, DNA-directed DNA polymerase

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Non-polymers , 3 types, 157 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 3.1 Å3/Da / Density % sol: 59.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, HEPES-sodium, calcium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2HEPES-sodium11
3calcium acetate11
4H2O11
5PEG 400012
6HEPES-sodium12
7calcium acetate12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 6, 2003 / Details: Confocat
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. all: 28078 / Num. obs: 28078 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.125
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.549 / % possible all: 86.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ASD

2asd


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.864 / SU B: 38.216 / SU ML: 0.351 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27851 1417 5.1 %RANDOM
Rwork0.22415 ---
all0.22705 26374 --
obs0.22705 26374 95.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.903 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20.98 Å2
2--2.82 Å20 Å2
3----2.4 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5478 1257 64 147 6946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227032
X-RAY DIFFRACTIONr_angle_refined_deg1.3622.2269722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.625680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7223.636242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.978151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0331548
X-RAY DIFFRACTIONr_chiral_restr0.0780.21108
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024686
X-RAY DIFFRACTIONr_nbd_refined0.2150.23506
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24690
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2320
X-RAY DIFFRACTIONr_metal_ion_refined0.1850.217
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.25
X-RAY DIFFRACTIONr_mcbond_it0.3261.53496
X-RAY DIFFRACTIONr_mcangle_it0.625518
X-RAY DIFFRACTIONr_scbond_it0.75834361
X-RAY DIFFRACTIONr_scangle_it1.4154.54204
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 91 -
Rwork0.355 1824 -
obs--91.1 %
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)
11.44960.33230.34190.63650.03272.1320.05930.18580.1775-0.0342-0.13330.0827-0.1832-0.2180.0739-0.18760.1306-0.0137-0.21890.0211-0.132614.7338-2.35291.4326
21.2119-0.4337-0.43251.19750.98065.0711-0.1015-0.3083-0.19740.2334-0.11250.18350.39190.57430.2139-0.11650.00360.0330.04920.0366-0.047433.067186.839657.6035
32.97122.47390.06163.0818-0.29910.4337-0.1002-0.38210.1627-0.0473-0.10570.1133-0.4295-0.01380.206-0.03790.0438-0.018-0.24840.0162-0.029523.47999.45556.1469
42.96792.44170.64345.99390.80560.15860.1585-0.5035-0.2310.3668-0.2678-0.10481.11260.27690.10930.33890.07760.10240.15970.1022-0.025424.863676.591664.6792
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AE1 - 3419 - 349
2X-RAY DIFFRACTION2BF1001 - 13419 - 349
3X-RAY DIFFRACTION3DA801 - 8131 - 13
4X-RAY DIFFRACTION3EB903 - 9193 - 19
5X-RAY DIFFRACTION3AO4141
6X-RAY DIFFRACTION3AG4151
7X-RAY DIFFRACTION3AH4161
8X-RAY DIFFRACTION3AI4171
9X-RAY DIFFRACTION3DJ4181
10X-RAY DIFFRACTION4HC1801 - 18131 - 13
11X-RAY DIFFRACTION4JD1901 - 19191 - 19
12X-RAY DIFFRACTION4BP14141
13X-RAY DIFFRACTION4BK14151
14X-RAY DIFFRACTION4BL14161
15X-RAY DIFFRACTION4BM14171

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