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- PDB-2hvi: ddCTP:G pair in the polymerase active site (0 position) -

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Basic information

Entry
Database: PDB / ID: 2hvi
TitleddCTP:G pair in the polymerase active site (0 position)
Components
  • 5'-D(*C*AP*TP*GP*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 / closed conformation / Transferase-DNA COMPLEX
Function / homology
Function and homology information


3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA repair / 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
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 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 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.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 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _struct_conn.pdbx_leaving_atom_flag
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.pdbx_number_of_molecules / _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.ptnr2_label_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 / _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(*C*AP*TP*GP*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(*C*AP*TP*GP*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)147,97314
Polymers145,7916
Non-polymers2,1838
Water11,746652
1
B: 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'
C: 5'-D(*C*AP*TP*GP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'
A: DNA Polymerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1647
Polymers72,8953
Non-polymers1,2694
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(*C*AP*TP*GP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'
D: DNA Polymerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8097
Polymers72,8953
Non-polymers9144
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.795, 108.492, 149.403
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 with a DNA polymerase molecule, a primer and template DNA, and an incoming ddCTP+Mg.

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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(*C*AP*TP*GP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'


Mass: 4016.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA template strand

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Protein / Sugars , 2 types, 4 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, 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 , 4 types, 658 molecules

#5: Chemical ChemComp-DCT / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE


Type: DNA linking / Mass: 451.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H16N3O12P3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 50% saturated ammonium sulfate, 2.5% MPD, 10 mM MgSO4, 100 mM MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2MPD11
3MES11
4MgSO411
5H2O11
6MgSO412
7ammonium sulfate12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 9, 2004 / 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: 93220 / Num. obs: 93220 / % possible obs: 87.4 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rsym value: 0.084 / Χ2: 1.023 / Net I/σ(I): 10.3
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.87 / Num. unique all: 8751 / Rsym value: 0.638 / Χ2: 0.941 / % possible all: 82.7

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Processing

Software
NameVersionClassificationNB
CNSrefinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
HKL-2000data reduction
CNSphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1LV5

1lv5


Resolution: 1.98→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.231 4484 4.2 %random
Rwork0.199 ---
all-93220 --
obs-88661 83.2 %-
Solvent computationBsol: 48.527 Å2
Displacement parametersBiso mean: 31.399 Å2
Baniso -1Baniso -2Baniso -3
1--0.925 Å20 Å20 Å2
2--2.77 Å20 Å2
3----1.845 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.98→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9304 850 134 652 10940
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.194
X-RAY DIFFRACTIONc_dihedral_angle_d21.95
X-RAY DIFFRACTIONc_improper_angle_d0.98984
LS refinement shellResolution: 1.98→2.05 Å
RfactorNum. reflection% reflection
Rfree0.295 371 -
Rwork0.2934 --
obs-7628 0.7209 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:dna-rna-multi-endo-new2.param
X-RAY DIFFRACTION4CNS_TOPPAR:ddctp.PAR
X-RAY DIFFRACTION5CNS_TOPPAR:sucrose.par

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