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- PDB-8scs: Bst DNA polymerase I Large Fragment wildtype D598A with 3'-amino ... -

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Basic information

Entry
Database: PDB / ID: 8scs
TitleBst DNA polymerase I Large Fragment wildtype D598A with 3'-amino primer, dGTP, and calcium time-resolved 8h
Components
  • DNA polymerase I
  • DNA primer/product
  • DNA template
KeywordsREPLICATION/DNA / DNA Polymerase / NP-DNA / Origin of Life / Time-Resolved Crystallography / REPLICATION-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 1 / 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 / Ribonuclease H superfamily ...DNA polymerase 1 / 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 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFang, Z. / Lelyveld, V.S. / Szostak, J.W.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Simons Foundation290363 United States
CitationJournal: Science / Year: 2023
Title: Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity.
Authors: Lelyveld, V.S. / Fang, Z. / Szostak, J.W.
History
DepositionApr 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase I
B: DNA primer/product
C: DNA template
D: DNA polymerase I
E: DNA primer/product
F: DNA template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,53022
Polymers146,1276
Non-polymers2,40316
Water4,828268
1
A: DNA polymerase I
B: DNA primer/product
C: DNA template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,36112
Polymers73,0633
Non-polymers1,2989
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: DNA polymerase I
E: DNA primer/product
F: DNA template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,16910
Polymers73,0633
Non-polymers1,1057
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.623, 108.676, 149.254
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein DNA polymerase I


Mass: 66057.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: DPO1 / Production host: Escherichia coli (E. coli) / References: UniProt: D9N168

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DNA chain , 2 types, 4 molecules BECF

#2: DNA chain DNA primer/product


Mass: 3069.032 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA template


Mass: 3936.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 284 molecules

#4: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 52.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2M ammonium sulphate, 0.1M MES pH 5.3-6.0, 20 mM CaCl2, 5% MPD
PH range: 5.3-6.0

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Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033175 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033175 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 89558 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 23.68 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.038 / Rrim(I) all: 0.095 / Χ2: 0.917 / Net I/σ(I): 19.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 4432 / CC1/2: 0.869 / CC star: 0.964 / Rpim(I) all: 0.223 / Rrim(I) all: 0.553 / Χ2: 0.817 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.24 Å / SU ML: 0.2325 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.0839
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2328 4632 5.18 %
Rwork0.1899 84712 -
obs0.1921 89344 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.05 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9290 900 132 268 10590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007210628
X-RAY DIFFRACTIONf_angle_d0.898214578
X-RAY DIFFRACTIONf_chiral_restr0.0511622
X-RAY DIFFRACTIONf_plane_restr0.0051708
X-RAY DIFFRACTIONf_dihedral_angle_d23.80264086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.30111530.23482543X-RAY DIFFRACTION90.8
2.12-2.140.26821450.2262776X-RAY DIFFRACTION99.32
2.14-2.170.27551410.21972833X-RAY DIFFRACTION99.77
2.17-2.20.29821410.22492814X-RAY DIFFRACTION99.9
2.2-2.230.28061720.21942791X-RAY DIFFRACTION99.83
2.23-2.260.31051460.22192798X-RAY DIFFRACTION99.8
2.26-2.290.26591650.20992805X-RAY DIFFRACTION99.87
2.29-2.320.26581480.20622804X-RAY DIFFRACTION99.9
2.32-2.360.28471600.20382799X-RAY DIFFRACTION99.97
2.36-2.40.27551250.20642863X-RAY DIFFRACTION99.97
2.4-2.440.27161450.20972822X-RAY DIFFRACTION99.97
2.44-2.480.29071620.21092817X-RAY DIFFRACTION99.97
2.48-2.530.25721580.20382805X-RAY DIFFRACTION99.93
2.53-2.580.26051660.21472805X-RAY DIFFRACTION99.9
2.58-2.640.3291400.22042826X-RAY DIFFRACTION99.83
2.64-2.70.26481340.22222827X-RAY DIFFRACTION99.83
2.7-2.770.29441810.21982821X-RAY DIFFRACTION99.8
2.77-2.840.30851660.22442828X-RAY DIFFRACTION100
2.84-2.930.27661570.22162848X-RAY DIFFRACTION99.83
2.93-3.020.23371730.20652771X-RAY DIFFRACTION99.7
3.02-3.130.23761470.2092851X-RAY DIFFRACTION99.7
3.13-3.260.24731650.20062813X-RAY DIFFRACTION99.6
3.26-3.40.24251490.18952833X-RAY DIFFRACTION99.3
3.4-3.580.20751450.1762846X-RAY DIFFRACTION98.97
3.58-3.810.19651530.16712810X-RAY DIFFRACTION98.44
3.81-4.10.16071580.15982842X-RAY DIFFRACTION98.85
4.1-4.510.1821570.14672853X-RAY DIFFRACTION98.95
4.51-5.170.17841660.15132880X-RAY DIFFRACTION99.25
5.17-6.510.1881730.17512902X-RAY DIFFRACTION99.77
6.51-45.240.18081410.15713086X-RAY DIFFRACTION99.69

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