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- PDB-2au0: Unmodified preinsertion binary complex -

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Basic information

Entry
Database: PDB / ID: 2au0
TitleUnmodified preinsertion binary complex
Components
  • 5'-D(*CP*TP*AP*AP*CP*G*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 / binary complex / 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
DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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.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*TP*AP*AP*CP*G*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*TP*AP*AP*CP*G*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)101,3029
Polymers101,1826
Non-polymers1203
Water2,126118
1
D: 5'-D(*GP*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*(DDG))-3'
E: 5'-D(*CP*TP*AP*AP*CP*G*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)50,6314
Polymers50,5913
Non-polymers401
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*TP*AP*AP*CP*G*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)50,6715
Polymers50,5913
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.644, 180.962, 51.571
Angle α, β, γ (deg.)90.00, 107.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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*TP*AP*AP*CP*G*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
#3: Protein Dpo4 polymerase IV / Pol IV


Mass: 40825.410 Da / Num. of mol.: 2
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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.4 Å3/Da / Density % sol: 48 %
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: Mar 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 27449 / Num. obs: 27449 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.096
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.635 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: OxoG-modified preinsertion binary complex; PDB ID code 2ASJ

2asj


Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.861 / SU B: 32.762 / SU ML: 0.362 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.455 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31026 1194 4.9 %RANDOM
Rwork0.26945 ---
obs0.27147 23377 99.73 %-
all-22707 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.464 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-1.01 Å2
2---1 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5478 1052 3 118 6651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226737
X-RAY DIFFRACTIONr_bond_other_d0.0020.025884
X-RAY DIFFRACTIONr_angle_refined_deg1.4942.1899276
X-RAY DIFFRACTIONr_angle_other_deg0.861313784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.785680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.20523.636242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.918151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9371548
X-RAY DIFFRACTIONr_chiral_restr0.0710.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026540
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021098
X-RAY DIFFRACTIONr_nbd_refined0.2340.31919
X-RAY DIFFRACTIONr_nbd_other0.1860.36887
X-RAY DIFFRACTIONr_nbtor_refined0.1990.53085
X-RAY DIFFRACTIONr_nbtor_other0.0880.53981
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3050.5417
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1490.512
X-RAY DIFFRACTIONr_metal_ion_refined0.3380.51
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.354
X-RAY DIFFRACTIONr_symmetry_vdw_other0.180.3120
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3160.56
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3551.53557
X-RAY DIFFRACTIONr_mcbond_other0.0591.51382
X-RAY DIFFRACTIONr_mcangle_it0.6125518
X-RAY DIFFRACTIONr_scbond_it0.74833988
X-RAY DIFFRACTIONr_scangle_it1.2044.53758
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 71 -
Rwork0.282 1708 -
obs--100 %
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)
11.36630.37950.83630.34330.04290.68470.0139-0.0051-0.04970.02590.019-0.0002-0.1011-0.0325-0.03290.03290.01030.0720.04650.0158-0.01145.3120.7614.397
20.16950.18460.36980.26090.22131.36250.042-0.0095-0.1066-0.02920.0003-0.0278-0.07180.0127-0.04220.01640.03410.0630.07070.00470.02372.719143.51527.777
33.65590.99092.63390.53681.15712.6298-0.0706-0.2147-0.2082-0.18290.1691-0.2066-0.6099-0.2867-0.09850.1781-0.07850.00970.11150.02930.131815.52210.45814.416
40.6711-0.31471.73121.4508-0.42434.58090.404-0.3675-0.44330.19770.1606-0.18170.3954-0.1536-0.56470.14020.07130.05470.1249-0.08440.1435-4.179133.7115.128
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 DIFFRACTION3EB907 - 9197 - 19
5X-RAY DIFFRACTION3AG4151
6X-RAY DIFFRACTION4HC1801 - 18131 - 13
7X-RAY DIFFRACTION4JD1907 - 19197 - 19
8X-RAY DIFFRACTION4HH14151
9X-RAY DIFFRACTION4JI14161

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