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- PDB-2asj: oxoG-modified Preinsertion Binary Complex -

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Basic information

Entry
Database: PDB / ID: 2asj
TitleoxoG-modified Preinsertion Binary Complex
Components
  • 5'-D(*CP*TP*AP*AP*CP*(8OG)*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'
  • DNA polymerase IV
Keywordstransferase/DNA / DNA polymerase / 8-oxoguanine / 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
DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 23, 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 / Refinement description / 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*TP*AP*AP*CP*(8OG)*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*(8OG)*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'
A: DNA polymerase IV
B: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3349
Polymers101,2146
Non-polymers1203
Water2,594144
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*(8OG)*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'
A: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6875
Polymers50,6073
Non-polymers802
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*(8OG)*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'
B: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6474
Polymers50,6073
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.219, 182.958, 52.209
Angle α, β, γ (deg.)90.00, 107.68, 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*(8OG)*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'


Mass: 5694.703 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: oxoG-modified Template Strand
#3: Protein DNA 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) / Gene: dbh, dpo4 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 49.5 %
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: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.991 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.991 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 40452 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.057
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.495 / % possible all: 88

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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: 2.35→20 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.881 / SU B: 30.371 / SU ML: 0.347 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.653 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The detwinned data is used for refinement. The twinning fraction is 0.4, detwinning operator is l, -k, h.
RfactorNum. reflection% reflectionSelection details
Rfree0.31751 1750 5.1 %RANDOM
Rwork0.24557 ---
obs0.24909 32562 88.74 %-
all-36438 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.44 Å2
Baniso -1Baniso -2Baniso -3
1-3.48 Å20 Å2-1.21 Å2
2---1.97 Å20 Å2
3----2.24 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5478 1052 3 144 6677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226737
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3812.1899276
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.975680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87623.636242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.951151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2931548
X-RAY DIFFRACTIONr_chiral_restr0.0810.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024566
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.22770
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24388
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2225
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2670.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.291
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4421.53512
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.76325518
X-RAY DIFFRACTIONr_scbond_it0.89933969
X-RAY DIFFRACTIONr_scangle_it1.4474.53758
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 110 -
Rwork0.353 1859 -
obs--69.31 %
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)
11.87540.17971.21711.39160.111.07150.0413-0.0538-0.0787-0.0232-0.0090.0997-0.1402-0.0234-0.0323-0.17140.05540.0577-0.04350.0178-0.16315.438-0.0154.203
20.443-0.18760.98970.4585-0.18222.95230.0316-0.0445-0.14920.00660.0299-0.0224-0.0613-0.0841-0.0615-0.11440.05060.0237-0.06980.0042-0.11332.174144.37728.21
39.81530.15284.62180.18220.61333.8061-0.1368-0.48980.7217-0.7182-0.04170.2474-0.8509-0.47580.17850.5039-0.1765-0.02780.03840.02850.231115.6749.84214.331
43.47051.18643.25611.6781-1.29417.60860.53010.1381-0.40760.5376-0.0834-0.1861.5753-0.2151-0.44680.45140.1539-0.08910.2523-0.15030.2063-4.421134.34615.204
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 341
2X-RAY DIFFRACTION2B1001 - 1341
3X-RAY DIFFRACTION3D801 - 813
4X-RAY DIFFRACTION3E907 - 919
5X-RAY DIFFRACTION3E416
6X-RAY DIFFRACTION4H1801 - 1813
7X-RAY DIFFRACTION4J1907 - 1919
8X-RAY DIFFRACTION4B1415

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