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- PDB-6ur4: DNA polymerase I Large Fragment from Bacillus stearothermophilus ... -

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Basic information

Entry
Database: PDB / ID: 6ur4
TitleDNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template and 3'-amino primer
Components
  • DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*(C42))-3')
  • DNA (5'-D(P*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3')
  • DNA polymerase I
KeywordsREPLICATION/DNA / amino primer / DNA polymerase / REPLICATION-DNA complex
Function / homology
Function and homology information


double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / 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. ...Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / 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-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsZhang, W. / Lelyveld, V.S. / Szostak, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase.
Authors: Lelyveld, V.S. / Zhang, W. / Szostak, J.W.
History
DepositionOct 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 (5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*(C42))-3')
C: DNA (5'-D(P*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)72,1763
Polymers72,1763
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-18 kcal/mol
Surface area27730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.608, 93.916, 106.124
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA polymerase I


Mass: 66101.766 Da / Num. of mol.: 1
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
#2: DNA chain DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*(C42))-3')


Mass: 2739.827 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3')


Mass: 3334.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
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: 2.96 Å3/Da / Density % sol: 62.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1 M Malonic acid, 0.15 M Ammonium citrate tribasic, 0.07 M Succinic acid, 0.18 M DL-Malic acid, 0.24 M Sodium acetate trihydrate, 0.3 M Sodium formate, 0.1 M Ammonium tartrate dibasic, pH 7.0

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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: MAR CCD 130 mm / Detector: CCD / Date: Dec 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 40025 / % possible obs: 94.4 % / Redundancy: 7 % / CC1/2: 0.978 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.057 / Rrim(I) all: 0.153 / Χ2: 1.422 / Net I/σ(I): 15.1
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 6 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 6.8 / Num. unique obs: 3455 / CC1/2: 0.802 / Rpim(I) all: 0.245 / Rrim(I) all: 0.628 / Χ2: 2.09 / % possible all: 83.2

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DSI

4dsi


Resolution: 2.25→28.4 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 1946 4.86 %RANDOM
Rwork0.2054 ---
obs0.2073 40004 94.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→28.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4649 406 0 164 5219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135187
X-RAY DIFFRACTIONf_angle_d1.8187093
X-RAY DIFFRACTIONf_dihedral_angle_d26.772005
X-RAY DIFFRACTIONf_chiral_restr0.084798
X-RAY DIFFRACTIONf_plane_restr0.011852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.30.3788960.36712159X-RAY DIFFRACTION76
2.3-2.370.29141600.23012821X-RAY DIFFRACTION100
2.37-2.430.29781450.21362825X-RAY DIFFRACTION100
2.43-2.510.21631610.20772819X-RAY DIFFRACTION100
2.51-2.60.26281500.21552850X-RAY DIFFRACTION100
2.6-2.710.28061440.22142834X-RAY DIFFRACTION100
2.71-2.830.32191280.23272887X-RAY DIFFRACTION100
2.83-2.980.30521410.23462876X-RAY DIFFRACTION100
2.98-3.170.28611310.23162865X-RAY DIFFRACTION100
3.17-3.410.24661530.21612878X-RAY DIFFRACTION100
3.41-3.750.2394880.22771943X-RAY DIFFRACTION67
3.75-4.290.20971530.18052377X-RAY DIFFRACTION83
4.29-5.40.17991270.15522924X-RAY DIFFRACTION99
5.41-28.40.19211690.15333000X-RAY DIFFRACTION98

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