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- PDB-6vdc: POL domain of Pol1 from M. smegmatis -

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Basic information

Entry
Database: PDB / ID: 6vdc
TitlePOL domain of Pol1 from M. smegmatis
ComponentsDNA polymerase I
KeywordsTRANSFERASE / mycobacteria / DNA polymerase / apoenzyme
Function / homology
Function and homology information


5'-3' exonuclease activity / 3'-5' exonuclease activity / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / metal ion binding
Similarity search - Function
: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / DNA polymerase 1 / Helix-hairpin-helix motif, class 2 ...: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / DNA polymerase 1 / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / 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 / PIN-like domain superfamily / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DNA polymerase I / DNA polymerase I
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
AuthorsShuman, S. / Goldgur, Y. / Ghosh, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P30-CA008748 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Mycobacterial DNA polymerase I: activities and crystal structures of the POL domain as apoenzyme and in complex with a DNA primer-template and of the full-length FEN/EXO-POL enzyme.
Authors: Ghosh, S. / Goldgur, Y. / Shuman, S.
History
DepositionDec 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 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

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Assembly

Deposited unit
A: DNA polymerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5332
Polymers66,4781
Non-polymers551
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-5 kcal/mol
Surface area23310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.591, 150.951, 150.348
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein DNA polymerase I


Mass: 66477.562 Da / Num. of mol.: 1 / Fragment: UNP residues 304-908
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: polA, MSMEI_3749
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: I7G3P9, UniProt: A0QYZ2*PLUS, DNA-directed DNA polymerase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium chloride, 20% PEG3350 / Temp details: ambient

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 31, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 28069 / % possible obs: 99.1 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rpim(I) all: 0.03 / Net I/σ(I): 33.6
Reflection shellResolution: 2.4→2.44 Å / Num. unique obs: 1368 / CC1/2: 0.869 / Rpim(I) all: 0.312

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4UQG

4uqg


Resolution: 2.402→45.83 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.3
RfactorNum. reflection% reflection
Rfree0.2655 3815 7.17 %
Rwork0.2192 --
obs0.2226 28056 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.31 Å2 / Biso mean: 69.5791 Å2 / Biso min: 33.15 Å2
Refinement stepCycle: final / Resolution: 2.402→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3838 0 1 81 3920
Biso mean--75.94 53.14 -
Num. residues----497
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4022-2.43260.3471340.2953173996
2.4326-2.46460.32821430.2686185899
2.4646-2.49830.31731360.2607181498
2.4983-2.5340.34671410.2812179798
2.534-2.57180.34511390.2588184399
2.5718-2.6120.35511420.26061838100
2.612-2.65480.30031390.25581823100
2.6548-2.70060.24361450.25061860100
2.7006-2.74970.28341410.24151829100
2.7497-2.80260.29531450.2441872100
2.8026-2.85980.38931380.25721849100
2.8598-2.9220.29751390.23471835100
2.922-2.98990.25581450.2383182899
2.9899-3.06470.31911410.23961841100
3.0647-3.14750.32591440.23391853100
3.1475-3.24010.28971390.24681827100
3.2401-3.34470.2911500.23411849100
3.3447-3.46420.26591460.22891844100
3.4642-3.60280.26041330.2173177898
3.6028-3.76670.28861470.2176181097
3.7667-3.96520.26431440.20881829100
3.9652-4.21350.26231380.1956183399
4.2135-4.53850.26171390.1856184499
4.5385-4.99480.23651390.1836181499
4.9948-5.71630.23461450.2091855100
5.7163-7.19750.23881390.2238180298
7.1975-45.830.21321440.2083180497

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