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

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Basic information

Entry
Database: PDB / ID: 8scr
TitleBst DNA polymerase I Large Fragment wildtype 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 / 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 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)148,62623
Polymers146,1276
Non-polymers2,49917
Water5,999333
1
A: DNA polymerase I
B: DNA primer/product
C: DNA template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,55314
Polymers73,0633
Non-polymers1,49011
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-100 kcal/mol
Surface area27290 Å2
MethodPISA
2
D: DNA polymerase I
E: DNA primer/product
F: DNA template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0739
Polymers73,0633
Non-polymers1,0096
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-65 kcal/mol
Surface area27210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.770, 109.083, 151.185
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, 350 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.: 11 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 53.51 %
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→50 Å / Num. obs: 101401 / % possible obs: 96.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 23.61 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.021 / Rrim(I) all: 0.053 / Χ2: 0.912 / Net I/σ(I): 34.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 5214 / CC1/2: 0.922 / CC star: 0.98 / Rpim(I) all: 0.188 / Rrim(I) all: 0.487 / Χ2: 0.879 / % 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→44.39 Å / SU ML: 0.2368 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.9917
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2364 5145 5.13 %
Rwork0.1943 95190 -
obs0.1965 100335 95.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.65 Å2
Refinement stepCycle: LAST / Resolution: 2→44.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9290 900 137 333 10660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007510649
X-RAY DIFFRACTIONf_angle_d0.931614610
X-RAY DIFFRACTIONf_chiral_restr0.0531625
X-RAY DIFFRACTIONf_plane_restr0.00511711
X-RAY DIFFRACTIONf_dihedral_angle_d24.58614100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.31131350.23792834X-RAY DIFFRACTION85.12
2.02-2.050.31551590.22893079X-RAY DIFFRACTION93.39
2.05-2.070.24681690.2183147X-RAY DIFFRACTION95.64
2.07-2.10.24251520.21533278X-RAY DIFFRACTION98.42
2.1-2.120.27041770.21343260X-RAY DIFFRACTION99.36
2.12-2.150.2531700.20983276X-RAY DIFFRACTION99.6
2.15-2.180.26221750.22083308X-RAY DIFFRACTION99.74
2.18-2.220.28161790.22313310X-RAY DIFFRACTION99.97
2.22-2.250.36291040.29591805X-RAY DIFFRACTION55.08
2.25-2.290.2993970.22992044X-RAY DIFFRACTION61.22
2.29-2.330.25641760.21533286X-RAY DIFFRACTION99.97
2.33-2.370.26352050.20483273X-RAY DIFFRACTION100
2.37-2.420.27831860.20213285X-RAY DIFFRACTION100
2.42-2.460.22911680.2063333X-RAY DIFFRACTION100
2.46-2.520.25351730.21053342X-RAY DIFFRACTION100
2.52-2.580.26472000.2063268X-RAY DIFFRACTION100
2.58-2.640.26721950.2073301X-RAY DIFFRACTION99.97
2.64-2.710.25082050.21763289X-RAY DIFFRACTION100
2.71-2.790.27481630.21813341X-RAY DIFFRACTION100
2.79-2.880.29641690.21673342X-RAY DIFFRACTION100
2.88-2.990.23851610.21843338X-RAY DIFFRACTION100
2.99-3.10.24122020.21053325X-RAY DIFFRACTION100
3.11-3.250.23251890.20933327X-RAY DIFFRACTION99.94
3.25-3.420.25491780.19263350X-RAY DIFFRACTION100
3.42-3.630.23521700.18363173X-RAY DIFFRACTION97.07
3.65-3.910.19931260.17012565X-RAY DIFFRACTION82.65
3.91-4.30.20271810.16263316X-RAY DIFFRACTION98.93
4.31-4.930.18682130.15573387X-RAY DIFFRACTION99.86
4.93-6.20.21951970.1713417X-RAY DIFFRACTION99.94
6.21-44.390.1661710.15773591X-RAY DIFFRACTION99.73

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