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- PDB-1xc9: Structure of a high-fidelity polymerase bound to a benzo[a]pyrene... -

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Basic information

Entry
Database: PDB / ID: 1xc9
TitleStructure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication
Components
  • DNA polymerase I
  • DNA primer strand
  • DNA template strand with benzo[a]pyrene adduct
KeywordsTRANSFERASE/DNA / DNA polymerase I / DNA replication / klenow fragment / benzo[a]pyrene / benzopyrene / DNA lesion / translation replication / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


5'-3' exonuclease activity / 3'-5' exonuclease activity / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 ...: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / PIN-like domain superfamily / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
sucrose / 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHsu, G.W. / Huang, X. / Luneva, N.P. / Geacintov, N.E. / Beese, L.S.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Structure of a High Fidelity DNA Polymerase Bound to a Benzo[a]pyrene Adduct That Blocks Replication
Authors: Hsu, G.W. / Huang, X. / Luneva, N.P. / Geacintov, N.E. / Beese, L.S.
#1: Journal: To be Published
Title: Observing translation synthesis of an aromatic amine DNA adduct by a high-fidelity DNA polymerase
Authors: Hsu, G.W. / Kiefer, J.R. / Becherel, O.J. / Fuchs, R.P.P. / Beese, L.S.
#2: Journal: Cell(Cambridge,Mass.) / Year: 2004
Title: Structures of Mismatch Replication Errors Observed in a DNA Polymerase
Authors: Johnson, S.J. / Beese, L.S.
History
DepositionSep 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
B: DNA primer strand
C: DNA template strand with benzo[a]pyrene adduct
A: DNA polymerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,81910
Polymers73,7643
Non-polymers1,0557
Water6,720373
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.752, 93.733, 104.512
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsExists as a monomer. One molecule per asymmetric unit

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Components

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DNA chain , 2 types, 2 molecules BC

#1: DNA chain DNA primer strand


Mass: 3141.052 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA template strand with benzo[a]pyrene adduct


Mass: 4449.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: see remark 400

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Protein / Sugars , 2 types, 2 molecules A

#3: Protein DNA polymerase I / E.C.2.7.7.7 / POL I


Mass: 66172.844 Da / Num. of mol.: 1 / Fragment: analogous to the E. coli klenow fragment
Source method: isolated from a genetically manipulated source
Details: see remark 400
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: pet-30A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PlysS / References: UniProt: P52026, DNA-directed DNA polymerase
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 379 molecules

#5: Chemical ChemComp-BAP / 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE


Mass: 304.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H16O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.82 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: Ammonium Sulfate, Magnesium Sulfate, MPD, MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2MGSO411
3MPD11
4MES11
5(NH4)2SO412
6MGSO412
7MPD12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 5, 2001
RadiationMonochromator: Nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→42.76 Å / Num. all: 71966 / Num. obs: 71966 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 23.1 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 20.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1LV5

1lv5


Resolution: 1.9→42.76 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2634280.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 3414 5.1 %RANDOM
Rwork0.221 ---
all0.2211 69297 --
obs0.2211 67114 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.8031 Å2 / ksol: 0.385435 e/Å3
Displacement parametersBiso mean: 35.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.55 Å20 Å20 Å2
2---4.86 Å20 Å2
3---0.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4650 443 67 373 5533
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it0.841.5
X-RAY DIFFRACTIONc_mcangle_it1.382
X-RAY DIFFRACTIONc_scbond_it1.252
X-RAY DIFFRACTIONc_scangle_it22.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.282 533 5.1 %
Rwork0.264 9837 -
obs--90.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA-MULTI-ENDO.PARAMDNA-RNA-MULTI-ENDO.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5SUCROSE.PARSUCROSE.TOP

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