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

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Basic information

Entry
Database: PDB / ID: 8scu
TitleBst DNA polymerase I Large Fragment wildtype D598A with 3'-amino primer, dGTP, and calcium time-resolved 48h (Product State)
Components
  • DNA polymerase I
  • DNA template
  • NP-extended DNA primer
KeywordsREPLICATION/DNA / DNA Polymerase / NP-DNA / Origin of Life / Time-Resolved Crystallography / 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: 2.38 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: NP-extended DNA primer
C: DNA template
D: DNA polymerase I
E: NP-extended DNA primer
F: DNA template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,63817
Polymers146,1276
Non-polymers1,51211
Water5,585310
1
A: DNA polymerase I
B: NP-extended DNA primer
C: DNA template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,85411
Polymers73,0633
Non-polymers7908
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: DNA polymerase I
E: NP-extended DNA primer
F: DNA template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7856
Polymers73,0633
Non-polymers7213
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.082, 109.164, 150.591
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 NP-extended DNA primer


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, 321 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-CA / CALCIUM ION


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


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
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: 2.38→50 Å / Num. obs: 61520 / % possible obs: 98.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 34.66 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.054 / Rrim(I) all: 0.121 / Χ2: 0.903 / Net I/σ(I): 11.8
Reflection shellResolution: 2.38→2.42 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3062 / CC1/2: 0.799 / CC star: 0.942 / Rpim(I) all: 0.253 / Rrim(I) all: 0.559 / Χ2: 0.776 / % possible all: 99.8

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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: 2.38→47.04 Å / SU ML: 0.2857 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.2524
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2391 3121 5.15 %
Rwork0.1868 57533 -
obs0.1896 60654 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.06 Å2
Refinement stepCycle: LAST / Resolution: 2.38→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9290 900 81 310 10581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007910558
X-RAY DIFFRACTIONf_angle_d0.947914470
X-RAY DIFFRACTIONf_chiral_restr0.05041616
X-RAY DIFFRACTIONf_plane_restr0.00561706
X-RAY DIFFRACTIONf_dihedral_angle_d23.56964064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.420.3042980.22942074X-RAY DIFFRACTION76.75
2.42-2.460.31451230.22632536X-RAY DIFFRACTION95.13
2.46-2.50.25161450.21622558X-RAY DIFFRACTION96.06
2.5-2.550.27031410.21352626X-RAY DIFFRACTION98.02
2.55-2.60.29941240.22842630X-RAY DIFFRACTION98.43
2.6-2.650.31531240.22562685X-RAY DIFFRACTION99.36
2.65-2.710.33161500.22612635X-RAY DIFFRACTION98.86
2.71-2.770.28191460.23542650X-RAY DIFFRACTION99.25
2.77-2.840.34171480.2292647X-RAY DIFFRACTION99.25
2.84-2.920.27561330.21162680X-RAY DIFFRACTION99.75
2.92-30.25231410.2112681X-RAY DIFFRACTION99.37
3-3.10.26351480.2062665X-RAY DIFFRACTION99.43
3.1-3.210.26351530.20452671X-RAY DIFFRACTION99.26
3.21-3.340.25471560.19762623X-RAY DIFFRACTION98.2
3.34-3.490.25851260.18712654X-RAY DIFFRACTION97.27
3.49-3.670.21041240.1842546X-RAY DIFFRACTION94.45
3.67-3.90.20011680.16972547X-RAY DIFFRACTION94.83
3.9-4.20.21791370.16052578X-RAY DIFFRACTION94.73
4.2-4.630.21421340.14912610X-RAY DIFFRACTION95.31
4.63-5.30.19541720.15772655X-RAY DIFFRACTION97.42
5.3-6.670.23461740.17572730X-RAY DIFFRACTION99.01
6.67-47.040.19341560.16172852X-RAY DIFFRACTION98.14

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