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- PDB-7r0t: Crystal structure of exonuclease ExnV1 -

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Basic information

Entry
Database: PDB / ID: 7r0t
TitleCrystal structure of exonuclease ExnV1
ComponentsExonuclease ExnV1
KeywordsVIRAL PROTEIN / exonuclease
Function / homologyTERBIUM(III) ION / THYMIDINE-5'-PHOSPHATE
Function and homology information
Biological speciesThermus phage TSP4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.194 Å
AuthorsWelin, M. / Svensson, A. / Hakansson, M. / Al-Karadaghi, S. / Jasilionis, A. / Linares-Pasten, J.A. / Wang, L. / 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 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exonuclease ExnV1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4579
Polymers36,7861
Non-polymers6728
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-54 kcal/mol
Surface area14270 Å2
Unit cell
Length a, b, c (Å)42.279, 54.11, 171.732
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Exonuclease ExnV1


Mass: 36785.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus phage TSP4 (virus) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 54 molecules

#2: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Tb
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.3 / Details: 0.1 M Bicine pH 9.3 30 % PEG Smear Low

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.6488 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6488 Å / Relative weight: 1
ReflectionResolution: 2.19→45.78 Å / Num. obs: 20566 / % possible obs: 98.1 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.04 / Rrim(I) all: 0.141 / Net I/σ(I): 12.5
Reflection shellResolution: 2.19→2.26 Å / Rmerge(I) obs: 3.187 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1650 / CC1/2: 0.792 / Rpim(I) all: 0.935 / Rrim(I) all: 3.325

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.194→45.78 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.918 / SU R Cruickshank DPI: 0.244 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.244 / SU Rfree Blow DPI: 0.209 / SU Rfree Cruickshank DPI: 0.21
RfactorNum. reflection% reflectionSelection details
Rfree0.2784 1005 -RANDOM
Rwork0.2345 ---
obs0.2366 20538 97.8 %-
Displacement parametersBiso mean: 62.27 Å2
Baniso -1Baniso -2Baniso -3
1--5.111 Å20 Å20 Å2
2---11.0649 Å20 Å2
3---16.1759 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.194→45.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2341 0 28 46 2415
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082419HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.93286HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d832SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes405HARMONIC5
X-RAY DIFFRACTIONt_it2419HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion303SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance10HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact1931SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion18.12
LS refinement shellResolution: 2.194→2.21 Å
RfactorNum. reflection% reflection
Rfree0.5311 18 -
Rwork0.4326 --
obs--82.22 %
Refinement TLS params.Origin x: 20.2496 Å / Origin y: 16.6061 Å / Origin z: 142.517 Å
111213212223313233
T0.2896 Å20.0166 Å20.0379 Å2--0.1859 Å2-0.0021 Å2---0.3091 Å2
L0.9158 °20.1919 °2-0.6192 °2-0 °2-0.1983 °2--3.5524 °2
S-0.0476 Å °0.1349 Å °0.4071 Å °0.1349 Å °-0.0404 Å °0.015 Å °0.4071 Å °0.015 Å °0.088 Å °
Refinement TLS groupSelection details: { A|0 - 296 }

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