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- PDB-2hw3: T:O6-methyl-guanine pair in the polymerase postinsertion site (-1... -

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Basic information

Entry
Database: PDB / ID: 2hw3
TitleT:O6-methyl-guanine pair in the polymerase postinsertion site (-1 basepair position)
Components
  • 5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*CP*TP*T)-3'
  • 5'-D(*GP*TP*A*CP*(6OG)P*AP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3'
  • DNA Polymerase I
KeywordsTransferase/DNA / DNA polymerase I / DNA replication / Klenow fragment / Protein-DNA complex / O6-methyl-guanine / Transferase-DNA COMPLEX
Function / homology
Function and homology information


double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
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 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 ...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 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / 3'-5' exonuclease / 3'-5' exonuclease domain / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / 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 / DNA / DNA (> 10) / DNA polymerase I / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.98 Å
AuthorsWarren, J.J. / Forsberg, L.J. / Beese, L.S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: The structural basis for the mutagenicity of O6-methyl-guanine lesions.
Authors: Warren, J.J. / Forsberg, L.J. / Beese, L.S.
History
DepositionJul 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE THE DNA POLYMERASE GENE WAS CLONED FROM AN ORGANISM THAT WAS CLASSIFIED AS A THERMOSTABLE ...SEQUENCE THE DNA POLYMERASE GENE WAS CLONED FROM AN ORGANISM THAT WAS CLASSIFIED AS A THERMOSTABLE STRAIN OF BACILLUS STEAROTHERMOPHILUS BY RIBOSOMAL RNA SEQUENCING. HOWEVER, THIS PARTICULAR GENE HAS MUCH GREATER HOMOLOGY WITH THE ANALOGOUS GENE FROM GEOBACILLUS KAUSTOPHILUS, UNP ACCESSION, Q5KWC1_GEOKA.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*CP*TP*T)-3'
C: 5'-D(*GP*TP*A*CP*(6OG)P*AP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3'
A: DNA Polymerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,70711
Polymers74,5173
Non-polymers1,1898
Water10,863603
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.098, 93.684, 105.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains one biological assembly.

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Components

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DNA chain , 2 types, 2 molecules BC

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


Mass: 3349.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA primer strand
#2: DNA chain 5'-D(*GP*TP*A*CP*(6OG)P*AP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3'


Mass: 4937.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA template strand

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Protein / Sugars , 2 types, 3 molecules A

#3: Protein DNA Polymerase I


Mass: 66230.953 Da / Num. of mol.: 1
Fragment: residues 299-876 (analogous to E Coli Klenow Fragment)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: polA / Plasmid: PUC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q5KWC1, UniProt: Q45458*PLUS, 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.: 2
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 , 3 types, 609 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 603 / 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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 45% saturated ammonium sulfate, 100mM MES, 2.5% MPD, 10mM MgSO4, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2MES11
3MPD11
4MgSO411
5H2O11
6ammonium sulfate12
7MPD12
8MgSO412
9H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Details: Yale 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: 1.98→50 Å / Num. all: 57765 / Num. obs: 57765 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rsym value: 0.096 / Χ2: 1.034 / Net I/σ(I): 11.45
Reflection shellResolution: 1.98→2.1 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 6637 / Rsym value: 0.254 / Χ2: 0.564 / % possible all: 67.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.98→45.88 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 4.616 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2907 5 %RANDOM
Rwork0.21 ---
all0.212 57765 --
obs-57765 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.247 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20 Å20 Å2
2---1.36 Å20 Å2
3----0.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.165 Å0.181 Å
Refinement stepCycle: LAST / Resolution: 1.98→45.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4650 487 72 603 5812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225347
X-RAY DIFFRACTIONr_angle_refined_deg1.2862.1077339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.6965579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.43624.217230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.36515872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0751538
X-RAY DIFFRACTIONr_chiral_restr0.0890.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023816
X-RAY DIFFRACTIONr_nbd_refined0.1710.32412
X-RAY DIFFRACTIONr_nbtor_refined0.3030.53646
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.5808
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.342
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.340.558
X-RAY DIFFRACTIONr_mcbond_it0.5421.53014
X-RAY DIFFRACTIONr_mcangle_it0.87424673
X-RAY DIFFRACTIONr_scbond_it1.23632822
X-RAY DIFFRACTIONr_scangle_it2.0844.52666
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 107 -
Rwork0.293 2375 -
obs-2482 100 %

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