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- PDB-6ur2: DNA polymerase I Large Fragment from Bacillus stearothermophilus ... -

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Basic information

Entry
Database: PDB / ID: 6ur2
TitleDNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template and primer containing an N3'-> P5' linkage
Components
  • DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*(C42)P*G)-3')
  • DNA (5'-D(P*AP*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3')
  • DNA polymerase I
KeywordsREPLICATION/DNA / NP linkage / DNA polymerase / 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 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A ...: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / 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: 2.27 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 21, 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)P*G)-3')
C: DNA (5'-D(P*AP*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)72,8183
Polymers72,8183
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-12 kcal/mol
Surface area27810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.197, 93.679, 107.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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)
Strain: Strain X / 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)P*G)-3')


Mass: 3069.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3')


Mass: 3647.393 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.: 100 / 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: 2.82 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 10mM MgCl2, 0.8 M Succinic acid 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: 2.27→50 Å / Num. obs: 39951 / % possible obs: 99.9 % / Redundancy: 8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.046 / Rrim(I) all: 0.129 / Χ2: 1.312 / Net I/σ(I): 17.9
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 8 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 3928 / CC1/2: 0.986 / Rpim(I) all: 0.192 / Rrim(I) all: 0.543 / Χ2: 0.986 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L5U

1l5u


Resolution: 2.27→40.85 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.508 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.293 / ESU R Free: 0.238
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2767 1970 4.9 %RANDOM
Rwork0.229 ---
obs0.2313 37883 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 148.36 Å2 / Biso mean: 42.616 Å2 / Biso min: 23.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 2.27→40.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4649 449 0 100 5198
Biso mean---37.12 -
Num. residues----601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135235
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174784
X-RAY DIFFRACTIONr_angle_refined_deg1.551.67163
X-RAY DIFFRACTIONr_angle_other_deg1.2811.65311092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9675578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13922.201268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.20715876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2651538
X-RAY DIFFRACTIONr_chiral_restr0.0770.2676
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025534
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021097
LS refinement shellResolution: 2.272→2.331 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 122 -
Rwork0.34 2548 -
all-2670 -
obs--91.03 %

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