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- PDB-8sck: Bst DNA polymerase I Large Fragment mutant F710Y/D598A with 3'-am... -

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Basic information

Entry
Database: PDB / ID: 8sck
TitleBst DNA polymerase I Large Fragment mutant F710Y/D598A with 3'-amino primer, dGTP, and calcium time-resolved 4h
Components
  • DNA polymerase I
  • DNA primer/product
  • DNA template
KeywordsREPLICATION/DNA / DNA Polymerase / NP-DNA / Origin of Life / Time-Resolved Crystallography / DNA BINDING PROTEIN / REPLICATION-DNA complex
Function / homology
Function and homology information


3'-5' exonuclease activity / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
: / DNA polymerase I, ribonuclease H-like domain / 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 I, ribonuclease H-like domain / 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: 2.3 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)147,98516
Polymers146,1596
Non-polymers1,82710
Water4,306239
1
A: DNA polymerase I
B: DNA primer/product
C: DNA template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,18510
Polymers73,0793
Non-polymers1,1057
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)73,8016
Polymers73,0793
Non-polymers7213
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.500, 108.932, 149.356
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: 66073.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: DPO1, polA / Production host: Escherichia coli (E. coli) / References: UniProt: D9N168, DNA-directed DNA polymerase

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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, 249 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.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 52.73 %
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: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 66713 / % possible obs: 97.6 % / Redundancy: 4.8 % / Biso Wilson estimate: 29.29 Å2 / CC1/2: 0.978 / CC star: 0.995 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.049 / Rrim(I) all: 0.109 / Χ2: 0.911 / Net I/σ(I): 12.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 3344 / CC1/2: 0.891 / CC star: 0.971 / Rpim(I) all: 0.216 / Rrim(I) all: 0.485 / Χ2: 0.831 / % 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: 2.3→39.63 Å / SU ML: 0.2816 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.0518
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2477 3316 5 %
Rwork0.1937 62952 -
obs0.1964 66268 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.62 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9292 900 102 239 10533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007710606
X-RAY DIFFRACTIONf_angle_d0.913114546
X-RAY DIFFRACTIONf_chiral_restr0.05031622
X-RAY DIFFRACTIONf_plane_restr0.00521708
X-RAY DIFFRACTIONf_dihedral_angle_d17.14814088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.27911380.21682521X-RAY DIFFRACTION94.73
2.33-2.370.28181320.21372650X-RAY DIFFRACTION98.86
2.37-2.40.32631310.20942645X-RAY DIFFRACTION99.5
2.4-2.440.29781430.21362665X-RAY DIFFRACTION99.47
2.44-2.490.271500.21032670X-RAY DIFFRACTION99.72
2.49-2.530.29251470.20742676X-RAY DIFFRACTION99.68
2.53-2.580.27651320.20632667X-RAY DIFFRACTION99.89
2.58-2.630.30361700.21642658X-RAY DIFFRACTION99.82
2.63-2.690.31121310.22172665X-RAY DIFFRACTION99.79
2.69-2.750.29311380.22412700X-RAY DIFFRACTION99.96
2.75-2.820.31441420.22352664X-RAY DIFFRACTION99.93
2.82-2.90.29421340.21632694X-RAY DIFFRACTION99.82
2.9-2.980.27341200.22162721X-RAY DIFFRACTION99.89
2.98-3.080.28921380.21272671X-RAY DIFFRACTION99.89
3.08-3.190.23111340.21422732X-RAY DIFFRACTION99.86
3.19-3.320.25921480.20242685X-RAY DIFFRACTION99.89
3.32-3.470.24261500.19892693X-RAY DIFFRACTION99.89
3.47-3.650.2841210.20762377X-RAY DIFFRACTION87.99
3.65-3.880.26131190.22492137X-RAY DIFFRACTION78.63
3.88-4.180.20141160.17391914X-RAY DIFFRACTION71
4.18-4.60.19661390.15532736X-RAY DIFFRACTION99.76
4.6-5.260.21241530.15392743X-RAY DIFFRACTION99.79
5.26-6.620.20771460.17322792X-RAY DIFFRACTION99.93
6.63-39.630.17941440.15482876X-RAY DIFFRACTION98.5

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