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- PDB-3eyz: Cocrystal structure of Bacillus fragment DNA polymerase I with du... -

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Basic information

Entry
Database: PDB / ID: 3eyz
TitleCocrystal structure of Bacillus fragment DNA polymerase I with duplex DNA (open form)
Components
  • 5'-D(*DAP*DTP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DAP*DGP*DGP*DA)-3'
  • 5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DGP*DC)-3'
  • DNA polymerase I
KeywordsTRANSFERASE/DNA / Protein-DNA complex / 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 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 ...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 / 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
Similarity search - Component
Biological speciesBacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsWarren, J.J. / Wu, E.Y. / Golosov, A.A. / Karplus, M. / Beese, L.S.
CitationJournal: Structure / Year: 2010
Title: The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis.
Authors: Golosov, A.A. / Warren, J.J. / Beese, L.S. / Karplus, M.
History
DepositionOct 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_conn_type / struct_ref_seq / 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 / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase I
B: 5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DGP*DC)-3'
C: 5'-D(*DAP*DTP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DAP*DGP*DGP*DA)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8417
Polymers73,2103
Non-polymers6304
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-54 kcal/mol
Surface area28250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.663, 94.053, 106.925
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain 5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DGP*DC)-3'


Mass: 2980.956 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA primer strand
#3: DNA chain 5'-D(*DAP*DTP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DAP*DGP*DGP*DA)-3'


Mass: 4040.647 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA template strand

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein DNA polymerase I


Mass: 66188.844 Da / Num. of mol.: 1 / Mutation: F710Y
Source method: isolated from a genetically manipulated source
Details: The enzyme comes from a bacterium isolated from an Idaho hot spring, which was identified as a strain of Bacillus stearothermophilus by 16S rRNA sequence analysis (Kiefer, J.R. et al., 1997 Structure 5:95-108)
Source: (gene. exp.) Bacillus stearothermophilus (bacteria) / Gene: POLA / Plasmid: pUC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P52026*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.: 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 , 2 types, 301 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.98 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: Ammonium Sulfate, MES, MPD, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium Sulfate11
2MES11
3MPD11
4Ammonium Sulfate12
5MES12
6MPD12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 25, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 49257 / % possible obs: 93.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.084 / Χ2: 1.11 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.181.90.40834830.98367
2.18-2.262.60.38342421.06382.4
2.26-2.373.20.35347461.1191.5
2.37-2.493.70.31450771.07397.8
2.49-2.654.20.26251961.06399.8
2.65-2.854.40.19652371.048100
2.85-3.144.40.13152321.021100
3.14-3.594.40.08552641.155100
3.59-4.524.40.06653131.28899.8
4.52-504.20.04154671.1598.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
CNSphasing
RefinementStarting model: PDB ENTRY 1L3S

1l3s


Resolution: 2.1→50 Å / FOM work R set: 0.845 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2297 4.4 %Inherited from free reflection list of PDB entry 1L3S
Rwork0.211 ---
all-51672 --
obs-45369 87.8 %-
Solvent computationBsol: 46.132 Å2
Displacement parametersBiso mean: 41.101 Å2
Baniso -1Baniso -2Baniso -3
1--8.973 Å20 Å20 Å2
2--6.493 Å20 Å2
3---2.48 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4655 466 38 298 5457
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.158
LS refinement shellResolution: 2.1→2.12 Å
RfactorNum. reflection
Rfree0.4623 38
Rwork0.2814 -
obs-576
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2dna-rna-multi-endo-new2.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4CNS_TOPPAR:sucrose.par
X-RAY DIFFRACTION5CNS_TOPPAR:water_rep.param

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