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- PDB-1n56: Y-family DNA polymerase Dpo4 in complex with DNA containing abasi... -

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Basic information

Entry
Database: PDB / ID: 1n56
TitleY-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion
Components
  • 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*AP*A)-3'
  • 5'-D(*TP*CP*AP*TP*(3DR)P*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / Y-family / DNA polymerase / DNA lesion bypass / protein-DNA complex / 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 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
ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLing, H. / Boudsocq, F. / Woodgate, R. / Yang, W.
Citation
Journal: Mol.Cell / Year: 2004
Title: Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts.
Authors: Ling, H. / Boudsocq, F. / Woodgate, R. / Yang, W.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: Crystal structure of a Y-familyDNA polymerase in action: a mechanism for error-prone and lesion-bypass replication
Authors: Ling, H. / Boudsocq, F. / Woodgate, R. / Yang, W.
History
DepositionNov 4, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 4, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / pdbx_entity_src_syn ...citation / pdbx_entity_src_syn / pdbx_struct_conn_angle / refine / struct_conn / struct_conn_type / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _refine.ls_percent_reflns_obs / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*AP*A)-3'
D: 5'-D(*TP*CP*AP*TP*(3DR)P*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
E: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*AP*A)-3'
F: 5'-D(*TP*CP*AP*TP*(3DR)P*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
A: DNA polymerase IV
B: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,33112
Polymers99,2046
Non-polymers1,1276
Water8,953497
1
C: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*AP*A)-3'
D: 5'-D(*TP*CP*AP*TP*(3DR)P*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
A: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1586
Polymers49,6023
Non-polymers5563
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*AP*A)-3'
F: 5'-D(*TP*CP*AP*TP*(3DR)P*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
B: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1746
Polymers49,6023
Non-polymers5723
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.016, 102.358, 105.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 4 molecules CEDF

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


Mass: 4418.892 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Template / Source: (synth.) synthetic construct (others)
#2: DNA chain 5'-D(*TP*CP*AP*TP*(3DR)P*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'


Mass: 4925.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: primer / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 2 molecules AB

#3: Protein DNA polymerase IV / E.C.2.7.7.7 / dpo4 / Pol IV / Repair DNA polymerase of the DinB/UmuC superfamily / dinP


Mass: 40257.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: dpo4 / Plasmid: pet22bB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q97W02

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Non-polymers , 4 types, 503 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.65 Å3/Da / Density % sol: 53.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% PEG 3350, 0.1M Hepes, 100mM calcium acetate, 2.5% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2Hepes11
3calcium acetate11
4glycerol11
5PEG 335012
6glycerol12
7calcium acetate12
8Hepes12

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200HB / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 15, 2001 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→29.9 Å / Num. all: 42232 / Num. obs: 39503 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Biso Wilson estimate: 64.4 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.399 / % possible all: 80

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JX4

1jx4


Resolution: 2.4→29.9 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 980 -RANDOM
Rwork0.225 ---
obs0.225 39503 93.6 %-
all-42232 --
Displacement parametersBiso mean: 66.7 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5486 1238 64 497 7285
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.27

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