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- PDB-7r0k: Crystal structure of Polymerase I from phage G20c -

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Basic information

Entry
Database: PDB / ID: 7r0k
TitleCrystal structure of Polymerase I from phage G20c
ComponentsDNA polymerase I
KeywordsVIRAL PROTEIN / DNA polymerase
Function / homology
Function and homology information


viral DNA genome replication / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A / 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
Biological speciesThermus phage G20c (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.972 Å
AuthorsWelin, M. / Svensson, A. / Hakansson, M. / Al-Karadaghi, S. / Linares-Pasten, J.A. / Jasilionis, A. / Nordberg Karlsson, E. / Ahlqvist, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)685778European Union
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Crystal structure of DNA polymerase I from Thermus phage G20c.
Authors: Ahlqvist, J. / Linares-Pasten, J.A. / Jasilionis, A. / Welin, M. / Hakansson, M. / Svensson, L.A. / Wang, L. / Watzlawick, H. / Aevarsson, A. / Fridjonsson, O.H. / Hreggvidsson, G.O. / ...Authors: Ahlqvist, J. / Linares-Pasten, J.A. / Jasilionis, A. / Welin, M. / Hakansson, M. / Svensson, L.A. / Wang, L. / Watzlawick, H. / Aevarsson, A. / Fridjonsson, O.H. / Hreggvidsson, G.O. / Ketelsen Striberny, B. / Glomsaker, E. / Lanes, O. / Al-Karadaghi, S. / Nordberg Karlsson, E.
History
DepositionFeb 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase I
B: DNA polymerase I


Theoretical massNumber of molelcules
Total (without water)167,2282
Polymers167,2282
Non-polymers00
Water0
1
A: DNA polymerase I


Theoretical massNumber of molelcules
Total (without water)83,6141
Polymers83,6141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA polymerase I


Theoretical massNumber of molelcules
Total (without water)83,6141
Polymers83,6141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)309.77, 98.011, 77.614
Angle α, β, γ (deg.)90, 98.9, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA polymerase I /


Mass: 83614.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus phage G20c (virus) / Gene: G20c_11 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L4BKI3

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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: 3.48 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.3 M AmSO4 0.1 M Tris PH 8 0.05 M Li2SO4 0.02 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.972→153.02 Å / Num. obs: 32681 / % possible obs: 68.9 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.039 / Rrim(I) all: 0.104 / Net I/σ(I): 12.3
Reflection shellResolution: 2.972→3.254 Å / Rmerge(I) obs: 1.379 / Num. unique obs: 1634 / CC1/2: 0.555 / Rpim(I) all: 0.548 / Rrim(I) all: 1.485 / % possible all: 14.6

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BWM,

4bwm


Resolution: 2.972→153.02 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.486
RfactorNum. reflection% reflectionSelection details
Rfree0.2602 1564 -RANDOM
Rwork0.2158 ---
obs0.2179 32681 68.9 %-
Displacement parametersBiso mean: 124.19 Å2
Baniso -1Baniso -2Baniso -3
1-4.038 Å20 Å21.7876 Å2
2---5.9044 Å20 Å2
3---1.8664 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: LAST / Resolution: 2.972→153.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11067 0 0 0 11067
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00911305HARMONIC2
X-RAY DIFFRACTIONt_angle_deg115344HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3947SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1917HARMONIC5
X-RAY DIFFRACTIONt_it11305HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1446SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact9149SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion19.8
LS refinement shellResolution: 2.972→3.14 Å
RfactorNum. reflection% reflection
Rfree0.3341 24 -
Rwork0.2902 --
obs--9.09 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4347-0.2177-0.04990.8404-0.14620.2497-0.0412-0.11240.0694-0.11240.1508-0.05040.0694-0.0504-0.10960.189-0.09170.1857-0.2248-0.03760.000272.582513.438820.9679
20.6618-0.27070.16971.315-0.14771.6870.0675-0.13860.2926-0.1386-0.1042-0.68170.2926-0.68170.0367-0.2385-0.1669-0.10890.08960.147-0.094433.812832.1554-8.0588
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 726
2X-RAY DIFFRACTION2{ B|* }B2 - 728

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