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- PDB-2hvh: ddCTP:O6MeG pair in the polymerase active site (0 position) -

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Basic information

Entry
Database: PDB / ID: 2hvh
TitleddCTP:O6MeG pair in the polymerase active site (0 position)
Components
  • 5'-D(*CP*A*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'
  • 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-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 / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / DNA polymerase I / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.492 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 28, 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.name
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_assembly_gen / pdbx_struct_conn_angle / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_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_assembly_gen.asym_id_list / _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_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 / _struct_asym.entity_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 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
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(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'
C: 5'-D(*CP*A*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'
E: 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'
F: 5'-D(*CP*A*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'
A: DNA Polymerase I
D: DNA Polymerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,33818
Polymers145,8196
Non-polymers2,51912
Water5,008278
1
B: 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'
C: 5'-D(*CP*A*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'
A: DNA Polymerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,38810
Polymers72,9093
Non-polymers1,4797
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'
F: 5'-D(*CP*A*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'
D: DNA Polymerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9508
Polymers72,9093
Non-polymers1,0415
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.060, 109.390, 151.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains two complete biological assemblies, each of which consists of a DNA polymerase, two DNA strands, and an incoming ddCTP + Mn.

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Components

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DNA chain , 2 types, 4 molecules BECF

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


Mass: 2675.775 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA primer strand
#2: DNA chain 5'-D(*CP*A*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'


Mass: 4030.650 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA template strand

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Protein / Sugars , 2 types, 5 molecules AD

#3: Protein DNA Polymerase I


Mass: 66202.945 Da / Num. of mol.: 2
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.: 3
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, 287 molecules

#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-DCT / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE


Type: DNA linking / Mass: 451.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O12P3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 55% saturated ammonium sulfate, 100 mM MES, 2.5% MPD, 10mM MnSO4, 10mM MgSO4, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2MPD11
3MES11
4MnSO411
5MgSO411
6H2O11
7MnSO412
8MgSO412
9ammonium sulfate12
10H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2006 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.492→47.298 Å / Num. all: 54569 / Num. obs: 54569 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.135 / Rsym value: 0.135 / Net I/σ(I): 11.4
Reflection shellResolution: 2.492→2.63 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 3.2 / Num. measured all: 36059 / Num. unique all: 7420 / Rsym value: 0.414 / % possible all: 93.3

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
XDSdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 2HHW

2hhw


Resolution: 2.492→47.298 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.883 / SU B: 10.804 / SU ML: 0.236 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.537 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2765 5.1 %RANDOM
Rwork0.201 ---
all0.204 54569 --
obs-54529 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.483 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å20 Å2
2--1.04 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.492→47.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9310 810 150 278 10548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210533
X-RAY DIFFRACTIONr_angle_refined_deg1.2692.09114429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.66251160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04624.205459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.757151752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.651576
X-RAY DIFFRACTIONr_chiral_restr0.0850.21632
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027570
X-RAY DIFFRACTIONr_nbd_refined0.2090.34691
X-RAY DIFFRACTIONr_nbtor_refined0.3160.57158
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.5753
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.373
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.524
X-RAY DIFFRACTIONr_mcbond_it0.4721.55958
X-RAY DIFFRACTIONr_mcangle_it0.82229352
X-RAY DIFFRACTIONr_scbond_it1.06635433
X-RAY DIFFRACTIONr_scangle_it1.8214.55076
LS refinement shellResolution: 2.492→2.557 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 196 -
Rwork0.303 3294 -
obs-3490 86.73 %

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