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

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Basic information

Entry
Database: PDB / ID: 8scq
TitleBst DNA polymerase I Large Fragment wildtype D598A with 3'-amino primer, dGTP, and calcium time-resolved 2h
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


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: 2.18 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 1, 2023Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Nov 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)149,10628
Polymers146,1276
Non-polymers2,97922
Water4,360242
1
A: DNA polymerase I
B: DNA primer/product
C: DNA template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,64915
Polymers73,0633
Non-polymers1,58612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-121 kcal/mol
Surface area27640 Å2
MethodPISA
2
D: DNA polymerase I
E: DNA primer/product
F: DNA template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,45713
Polymers73,0633
Non-polymers1,39410
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8370 Å2
ΔGint-111 kcal/mol
Surface area27340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.657, 108.549, 148.248
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, 264 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.: 16 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.58 Å3/Da / Density % sol: 52.3 %
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: 2.18→50 Å / Num. obs: 78539 / % possible obs: 98.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 29.86 Å2 / CC1/2: 0.99 / CC star: 0.998 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.041 / Rrim(I) all: 0.104 / Χ2: 0.991 / Net I/σ(I): 19.2
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 3916 / CC1/2: 0.886 / CC star: 0.969 / Rpim(I) all: 0.21 / Rrim(I) all: 0.539 / Χ2: 0.823 / % 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: 2.18→46.83 Å / SU ML: 0.266 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.3569
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2356 3953 5.07 %
Rwork0.1881 74076 -
obs0.1905 78029 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.53 Å2
Refinement stepCycle: LAST / Resolution: 2.18→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9290 900 162 242 10594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007610669
X-RAY DIFFRACTIONf_angle_d0.907214640
X-RAY DIFFRACTIONf_chiral_restr0.05081625
X-RAY DIFFRACTIONf_plane_restr0.00511711
X-RAY DIFFRACTIONf_dihedral_angle_d24.74454100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.210.31451500.23452639X-RAY DIFFRACTION99.5
2.21-2.230.33321350.24922600X-RAY DIFFRACTION98.13
2.23-2.260.35671130.29681934X-RAY DIFFRACTION73.03
2.26-2.290.33371370.22532597X-RAY DIFFRACTION97.68
2.29-2.330.29661450.22432647X-RAY DIFFRACTION100
2.33-2.360.25921280.21082690X-RAY DIFFRACTION99.89
2.36-2.40.24961400.21172673X-RAY DIFFRACTION99.93
2.4-2.440.27431530.20862618X-RAY DIFFRACTION99.53
2.44-2.480.29051300.20472696X-RAY DIFFRACTION99.96
2.48-2.530.25391310.19872683X-RAY DIFFRACTION100
2.53-2.570.25521420.20462660X-RAY DIFFRACTION100
2.57-2.630.2831500.21272664X-RAY DIFFRACTION100
2.63-2.680.29181360.21042680X-RAY DIFFRACTION100
2.68-2.750.25021530.2162688X-RAY DIFFRACTION100
2.75-2.820.26491440.21762661X-RAY DIFFRACTION100
2.82-2.890.30831570.21312664X-RAY DIFFRACTION100
2.89-2.980.24551300.2152685X-RAY DIFFRACTION100
2.98-3.070.23341370.20252697X-RAY DIFFRACTION100
3.07-3.180.28131410.20352697X-RAY DIFFRACTION100
3.18-3.310.21431540.1932684X-RAY DIFFRACTION100
3.31-3.460.26491440.18272686X-RAY DIFFRACTION99.89
3.46-3.640.21891270.17542558X-RAY DIFFRACTION94.24
3.64-3.870.1931170.16912450X-RAY DIFFRACTION89.32
3.87-4.170.20181450.15772691X-RAY DIFFRACTION98.95
4.17-4.590.19041390.14872735X-RAY DIFFRACTION99.97
4.59-5.250.19121600.15552719X-RAY DIFFRACTION99.93
5.25-6.610.19111600.17912773X-RAY DIFFRACTION99.97
6.61-46.830.20411550.16452907X-RAY DIFFRACTION99.97

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