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- PDB-3gij: Dpo4 extension ternary complex with oxoG(syn)-A(anti) and oxoG(an... -

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Basic information

Entry
Database: PDB / ID: 3gij
TitleDpo4 extension ternary complex with oxoG(syn)-A(anti) and oxoG(anti)-A(syn) pairs
Components
  • 5'-D(*CP*TP*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*C)-3'
  • 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3'
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / DNA POLYMERASE / 8-OXOGUANINE / Y-FAMILY / LESION BYPASS / 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'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRechkoblit, O. / Malinina, L. / Patel, D.J.
CitationJournal: Structure / Year: 2009
Title: Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases.
Authors: Rechkoblit, O. / Malinina, L. / Cheng, Y. / Geacintov, N.E. / Broyde, S. / Patel, D.J.
History
DepositionMar 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 7, 2011Group: Database references
Revision 1.3Sep 6, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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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*(2DA))-3'
E: 5'-D(*CP*TP*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*C)-3'
B: DNA polymerase IV
H: 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3'
J: 5'-D(*CP*TP*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,09814
Polymers96,8436
Non-polymers1,2558
Water4,396244
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(*CP*TP*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0497
Polymers48,4223
Non-polymers6274
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-28.7 kcal/mol
Surface area19850 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(*CP*TP*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0497
Polymers48,4223
Non-polymers6274
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-31.5 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.264, 107.409, 97.867
Angle α, β, γ (deg.)90.000, 100.540, 90.000
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
#3: DNA chain 5'-D(*CP*TP*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*C)-3'


Mass: 5405.521 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA OXOG-modified template strand

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Non-polymers , 3 types, 252 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES, 100 mM Calcium acetate, 10% PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2Calcium acetate12
3PEG 400013

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2005
Details: 6144 x 6144 pixel elements with an effective pixel size less than 60x60 micron and resolution of order 90x90 micron
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. obs: 40120 / % possible obs: 92.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 20.1
Reflection shellResolution: 2.35→2.42 Å / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 1.8 / % possible all: 62.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GII

3gii


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 17.44 / SU ML: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.472 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1950 5.1 %RANDOM
Rwork0.209 ---
obs0.212 38605 94.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.64 Å2 / Biso mean: 61.17 Å2 / Biso min: 17.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å20 Å23.23 Å2
2---0.04 Å20 Å2
3---2.76 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5480 1180 68 244 6972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227029
X-RAY DIFFRACTIONr_angle_refined_deg1.6012.2229700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1915682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89523.621243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.787151121
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3051548
X-RAY DIFFRACTIONr_chiral_restr0.1250.21103
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024705
X-RAY DIFFRACTIONr_nbd_refined0.2430.34324
X-RAY DIFFRACTIONr_nbtor_refined0.3350.54742
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2550.5746
X-RAY DIFFRACTIONr_metal_ion_refined0.1840.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.3122
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3320.522
X-RAY DIFFRACTIONr_mcbond_it0.6171.53482
X-RAY DIFFRACTIONr_mcangle_it0.83625529
X-RAY DIFFRACTIONr_scbond_it1.40234401
X-RAY DIFFRACTIONr_scangle_it1.8354.54171
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 95 -
Rwork0.267 1987 -
all-2082 -
obs--69.82 %
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)
13.4061-0.9851-0.21382.34320.29171.6964-0.0781-0.3154-0.14990.1960.13090.062-0.07530.1774-0.0528-0.3253-0.00540.0349-0.30270.0033-0.216912.30221.35162.6298
23.9334-0.1365-0.43821.5622-1.19062.90380.0738-0.6451-0.08440.5037-0.04840.1225-0.40260.0765-0.02540.0198-0.09980.03040.0414-0.0697-0.2689-6.851355.793238.1771
30.84120.1551-1.33662.43790.49442.3517-0.3812-0.8919-0.36880.76340.3207-0.15-0.09380.52790.0605-0.00930.1296-0.09350.23980.11790.01220.4268-7.062312.1054
45.4159-1.7647-3.7866.15651.09715.1614-0.4963-1.5869-0.7871.21430.1872-1.01730.33751.20870.30910.06930.0358-0.20950.64310.24730.21674.18346.095745.3566
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 DIFFRACTION3E901 - 918
5X-RAY DIFFRACTION3A414
6X-RAY DIFFRACTION4H1802 - 1814
7X-RAY DIFFRACTION4J1905 - 1918
8X-RAY DIFFRACTION4B1414

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