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

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Basic information

Entry
Database: PDB / ID: 8scg
TitleBst DNA polymerase I Large Fragment mutant F710Y/D598A with 3'-amino primer, dGTP, and calcium time-resolved 0h (Ground State)
Components
  • 3'-Amino DNA Primer
  • DNA Tempelate
  • DNA polymerase I
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 / 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 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: 3'-Amino DNA Primer
C: DNA Tempelate
D: DNA polymerase I
E: 3'-Amino DNA Primer
F: DNA Tempelate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,97914
Polymers145,5006
Non-polymers1,4798
Water8,413467
1
A: DNA polymerase I
B: 3'-Amino DNA Primer
C: DNA Tempelate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6829
Polymers72,7503
Non-polymers9326
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: DNA polymerase I
E: 3'-Amino DNA Primer
F: DNA Tempelate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2975
Polymers72,7503
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.679, 108.814, 149.552
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 3'-Amino DNA Primer


Mass: 2739.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA Tempelate


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

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Non-polymers , 4 types, 475 molecules

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


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2 M ammonium sulphate, 0.1 M 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→50 Å / Num. obs: 99476 / % possible obs: 96.5 % / Redundancy: 9 % / Biso Wilson estimate: 26.62 Å2 / CC1/2: 0.981 / CC star: 0.995 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.039 / Rrim(I) all: 0.116 / Χ2: 1.011 / Net I/σ(I): 16.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 5.7 / Num. unique obs: 6410 / CC1/2: 0.918 / CC star: 0.979 / Rpim(I) all: 0.162 / Rrim(I) all: 0.479 / Χ2: 0.741 / % possible all: 88.4

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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→45.32 Å / SU ML: 0.2206 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.5402
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2452 4880 5.04 %
Rwork0.2022 91942 -
obs0.2044 96822 93.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.44 Å2
Refinement stepCycle: LAST / Resolution: 2→45.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9292 856 84 467 10699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007210500
X-RAY DIFFRACTIONf_angle_d0.906814386
X-RAY DIFFRACTIONf_chiral_restr0.05281608
X-RAY DIFFRACTIONf_plane_restr0.0051704
X-RAY DIFFRACTIONf_dihedral_angle_d23.93924050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.30411180.23232495X-RAY DIFFRACTION76.47
2.02-2.050.25041820.21483172X-RAY DIFFRACTION98.16
2.05-2.070.29391610.21213185X-RAY DIFFRACTION98.61
2.07-2.10.27871820.20483219X-RAY DIFFRACTION98.84
2.1-2.130.26631710.21023222X-RAY DIFFRACTION99.36
2.13-2.150.26311730.20713214X-RAY DIFFRACTION99.24
2.15-2.190.29951790.22743222X-RAY DIFFRACTION99.33
2.19-2.220.39221560.38072500X-RAY DIFFRACTION77.82
2.22-2.250.5053240.4485469X-RAY DIFFRACTION14.6
2.25-2.290.44621000.37251989X-RAY DIFFRACTION60.78
2.29-2.330.24781650.21313239X-RAY DIFFRACTION99.53
2.33-2.370.28161780.2043236X-RAY DIFFRACTION99.22
2.37-2.420.25311850.20083246X-RAY DIFFRACTION99.59
2.42-2.470.24551770.20613237X-RAY DIFFRACTION99.62
2.47-2.520.24471690.21173253X-RAY DIFFRACTION99.65
2.52-2.580.25121740.21233239X-RAY DIFFRACTION99.65
2.58-2.640.29071580.21153274X-RAY DIFFRACTION99.91
2.64-2.710.27761810.21863279X-RAY DIFFRACTION99.63
2.71-2.790.24931580.21913258X-RAY DIFFRACTION99.68
2.79-2.880.24251830.21913269X-RAY DIFFRACTION99.71
2.88-2.990.3021670.22263272X-RAY DIFFRACTION99.8
2.99-3.110.25921720.21573277X-RAY DIFFRACTION99.71
3.11-3.250.27711660.20613294X-RAY DIFFRACTION99.88
3.25-3.420.24121650.20513303X-RAY DIFFRACTION99.77
3.42-3.630.20441670.18593245X-RAY DIFFRACTION98.16
3.63-3.910.22181850.19673054X-RAY DIFFRACTION92.75
3.91-4.310.1951640.16813260X-RAY DIFFRACTION97.52
4.31-4.930.19621870.15883317X-RAY DIFFRACTION99.55
4.93-6.210.21661750.18153361X-RAY DIFFRACTION99.47
6.21-45.320.22551580.18343342X-RAY DIFFRACTION94.01

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