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- PDB-6vnp: Crystal structure of DPO4 extension past 8-oxoadenine (oxoA) and dT -

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Basic information

Entry
Database: PDB / ID: 6vnp
TitleCrystal structure of DPO4 extension past 8-oxoadenine (oxoA) and dT
Components
  • DNA (5'-D(*TP*TP*CP*AP*T*(R5M)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
  • DNA (5'-D(P*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*T)-3')
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / DPO4 / Y-family DNA polymerase / Translesion synthesis / TRANSFERASE / extension / 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
Chem-DZ4 / DNA / DNA (> 10) / DNA polymerase IV / DNA polymerase IV
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsJung, H. / Lee, S.
CitationJournal: To Be Published
Title: Crystal structure of DPO4 extension past 8-oxoadenine (oxoA) and dT
Authors: Jung, H. / Lee, S.
History
DepositionJan 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
P: DNA (5'-D(P*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*T)-3')
T: DNA (5'-D(*TP*TP*CP*AP*T*(R5M)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
A: DNA polymerase IV
B: DNA (5'-D(P*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*T)-3')
C: DNA (5'-D(*TP*TP*CP*AP*T*(R5M)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
D: DNA polymerase IV
E: DNA (5'-D(P*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*T)-3')
F: DNA (5'-D(*TP*TP*CP*AP*T*(R5M)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
G: DNA polymerase IV
H: DNA (5'-D(P*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*T)-3')
I: DNA (5'-D(*TP*TP*CP*AP*T*(R5M)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
J: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,60424
Polymers196,44812
Non-polymers2,15512
Water6,539363
1
P: DNA (5'-D(P*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*T)-3')
T: DNA (5'-D(*TP*TP*CP*AP*T*(R5M)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
A: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6516
Polymers49,1123
Non-polymers5393
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-51 kcal/mol
Surface area20350 Å2
MethodPISA
2
B: DNA (5'-D(P*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*T)-3')
C: DNA (5'-D(*TP*TP*CP*AP*T*(R5M)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
D: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6516
Polymers49,1123
Non-polymers5393
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-52 kcal/mol
Surface area20650 Å2
MethodPISA
3
E: DNA (5'-D(P*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*T)-3')
F: DNA (5'-D(*TP*TP*CP*AP*T*(R5M)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
G: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6516
Polymers49,1123
Non-polymers5393
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-51 kcal/mol
Surface area20230 Å2
MethodPISA
4
H: DNA (5'-D(P*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*T)-3')
I: DNA (5'-D(*TP*TP*CP*AP*T*(R5M)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
J: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6516
Polymers49,1123
Non-polymers5393
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-50 kcal/mol
Surface area20450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.255, 98.984, 102.875
Angle α, β, γ (deg.)90.030, 89.990, 89.920
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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DNA chain , 2 types, 8 molecules PBEHTCFI

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


Mass: 4400.863 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain
DNA (5'-D(*TP*TP*CP*AP*T*(R5M)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')


Mass: 5691.685 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein , 1 types, 4 molecules ADGJ

#3: Protein
DNA polymerase IV / Pol IV


Mass: 39019.523 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus (archaea)
Gene: dbh, SSOP1_2570, SULA_0242, SULB_0243, SULC_0242, SULG_01230, SULH_01230, SULI_01230, SULM_01230, SULN_01230, SULO_01240, SULZ_01250
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0E3K6E9, UniProt: Q97W02*PLUS, DNA-directed DNA polymerase

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Non-polymers , 3 types, 375 molecules

#4: Chemical
ChemComp-DZ4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine


Mass: 490.197 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O11P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50 mM Tris 7.5 20% PEG3350 100 mM Magnesium Acetate

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. obs: 78571 / % possible obs: 97.6 % / Redundancy: 1.9 % / Rpim(I) all: 0.061 / Net I/σ(I): 8.1
Reflection shellResolution: 2.42→2.47 Å / Num. unique obs: 4003 / CC1/2: 0.644 / Rpim(I) all: 0.454

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JX4

1jx4


Resolution: 2.42→47.3 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2416 3770 4.82 %
Rwork0.1994 --
obs-78203 97.69 %
Displacement parametersBiso mean: 47.48 Å2
Refinement stepCycle: LAST / Resolution: 2.42→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10972 2557 128 363 14020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010314107
X-RAY DIFFRACTIONf_angle_d1.271219506
X-RAY DIFFRACTIONf_chiral_restr0.09882231
X-RAY DIFFRACTIONf_plane_restr0.00692021
X-RAY DIFFRACTIONf_dihedral_angle_d25.74735817
LS refinement shellResolution: 2.42→2.45 Å
RfactorNum. reflection% reflection
Rfree0.2873 109 -
Rwork0.2601 2658 -
obs--96 %

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