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- PDB-4tqr: Ternary complex of Y-family DNA polymerase Dpo4 with (5'S)-8,5'-C... -

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Basic information

Entry
Database: PDB / ID: 4tqr
TitleTernary complex of Y-family DNA polymerase Dpo4 with (5'S)-8,5'-Cyclo-2'-deoxyguanosine and dTTP
Components
  • DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*T)-3')
  • DNA (5'-D(*TP*CP*AP*CP*(2LF)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / Y family DNA polymerase / DNA damage / cyclopurine / translesion synthesis / 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',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE / THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.58 Å
AuthorsZhao, L.
CitationJournal: Biochemistry / Year: 2015
Title: Kinetic and Structural Mechanisms of (5'S)-8,5'-Cyclo-2'-deoxyguanosine-Induced DNA Replication Stalling.
Authors: Xu, W. / Ouellette, A.M. / Wawrzak, Z. / Shriver, S.J. / Anderson, S.M. / Zhao, L.
History
DepositionJun 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Feb 4, 2015Group: Database references
Revision 1.3Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_symm_contact / refine_hist / struct_conn / struct_conn_type / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _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 / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase IV
P: DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*T)-3')
T: DNA (5'-D(*TP*CP*AP*CP*(2LF)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,25310
Polymers48,3273
Non-polymers9267
Water10,106561
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-79 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.537, 89.406, 112.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase IV / Pol IV


Mass: 39148.637 Da / Num. of mol.: 1 / Fragment: UNP residues 1-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: dbh, dpo4, SSO2448 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97W02, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules PT

#2: DNA chain DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*T)-3')


Mass: 3807.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*CP*AP*CP*(2LF)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')


Mass: 5370.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 568 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DOC / 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 291.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O6P
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 3.04 Å3/Da / Density % sol: 59.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 200 microM Dpo4, 240 microM primer-template DNA complex, 5 mM MgCl2, 1 mM dTTP, 20 mM Tris-HCl (pH 7.4), 60 mM NaCl, 2% glycerol (v/v), and 5 mM 2-mercaptoethanol were incubated at 37 C for ...Details: 200 microM Dpo4, 240 microM primer-template DNA complex, 5 mM MgCl2, 1 mM dTTP, 20 mM Tris-HCl (pH 7.4), 60 mM NaCl, 2% glycerol (v/v), and 5 mM 2-mercaptoethanol were incubated at 37 C for 5 min. Droplets (a 1:1 mixture of Dpo4-DNA complex mixture and the reservoir solution, v/v) were equilibrated against a reservoir solution containing 0.1M Tris-HCl (pH 7.4), 13% polyethylene glycol 3350 (w/v), 0.1 M Ca(CH3COO)2, and 2% glycerol (v/v).

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→28.32 Å / Num. obs: 81191 / % possible obs: 99.7 % / Redundancy: 5.5 % / Net I/σ(I): 23
Reflection shellResolution: 1.58→1.6 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.9_1690)refinement
RefinementResolution: 1.58→28.32 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2022 4024 4.96 %
Rwork0.182 77167 -
obs0.183 81191 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.29 Å2 / Biso mean: 34.1726 Å2 / Biso min: 8.67 Å2
Refinement stepCycle: final / Resolution: 1.58→28.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2658 609 52 561 3880
Biso mean--27.99 45 -
Num. residues----372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073440
X-RAY DIFFRACTIONf_angle_d1.1584764
X-RAY DIFFRACTIONf_chiral_restr0.045546
X-RAY DIFFRACTIONf_plane_restr0.005487
X-RAY DIFFRACTIONf_dihedral_angle_d18.7551350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.59860.24061190.2392649X-RAY DIFFRACTION100
1.5986-1.61810.24041440.22782623X-RAY DIFFRACTION100
1.6181-1.63860.26871350.22142627X-RAY DIFFRACTION100
1.6386-1.66010.2151340.21222627X-RAY DIFFRACTION100
1.6601-1.68290.24821420.20542644X-RAY DIFFRACTION100
1.6829-1.70690.22851540.19482632X-RAY DIFFRACTION100
1.7069-1.73240.21991390.19992649X-RAY DIFFRACTION100
1.7324-1.75940.2281580.2012614X-RAY DIFFRACTION100
1.7594-1.78830.23191350.1952650X-RAY DIFFRACTION100
1.7883-1.81910.22551370.19432639X-RAY DIFFRACTION100
1.8191-1.85220.191500.192605X-RAY DIFFRACTION100
1.8522-1.88780.22671360.1992702X-RAY DIFFRACTION100
1.8878-1.92630.22191270.18962600X-RAY DIFFRACTION100
1.9263-1.96820.22541120.19172691X-RAY DIFFRACTION100
1.9682-2.0140.19471610.18712659X-RAY DIFFRACTION100
2.014-2.06430.22411390.18912643X-RAY DIFFRACTION100
2.0643-2.12010.19381260.18842664X-RAY DIFFRACTION100
2.1201-2.18250.1771370.17472687X-RAY DIFFRACTION100
2.1825-2.25290.18011240.18072658X-RAY DIFFRACTION100
2.2529-2.33340.17871320.18172662X-RAY DIFFRACTION100
2.3334-2.42680.21741410.18682694X-RAY DIFFRACTION100
2.4268-2.53720.2191450.19042664X-RAY DIFFRACTION100
2.5372-2.67080.21311470.19532684X-RAY DIFFRACTION100
2.6708-2.8380.23481460.19232646X-RAY DIFFRACTION100
2.838-3.05690.1971550.20042715X-RAY DIFFRACTION100
3.0569-3.36410.18521350.17672699X-RAY DIFFRACTION100
3.3641-3.84980.18341370.16472727X-RAY DIFFRACTION100
3.8498-4.84640.19451530.15042735X-RAY DIFFRACTION99
4.8464-28.32840.19041240.18092678X-RAY DIFFRACTION92
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)
11.72190.489-0.69410.8298-0.26920.8388-0.10840.1725-0.0348-0.14580.0529-0.04110.1593-0.00680.03160.16230.0124-0.03460.14610.00280.112933.270788.707316.1749
22.0402-0.1989-1.94530.23410.20191.43230.00430.47380.1213-0.22350.0783-0.08080.029-0.2056-0.09910.2193-0.01540.0570.318-0.01020.192343.368892.96063.1639
32.4669-0.5239-2.71110.82621.0073.0218-0.2576-0.25460.0003-0.12110.16350.01960.37850.14170.12830.31150.00570.05860.37690.0270.173247.856589.9794-3.2496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A1 - 342
2X-RAY DIFFRACTION2chain 'T'T1 - 18
3X-RAY DIFFRACTION3chain 'P'P1 - 13

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