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- PDB-6we1: Wheat dwarf virus Rep domain complexed with a single-stranded DNA... -

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Basic information

Entry
Database: PDB / ID: 6we1
TitleWheat dwarf virus Rep domain complexed with a single-stranded DNA 8-mer comprising the cleavage site
Components
  • DNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*C)-3')
  • Replication-associated protein
KeywordsREPLICATION/DNA / HUH-tag / HUH motif / replicase / viral protein / single stranded DNA / ssDNA / ssDNA binding / REPLICATION / DNA BINDING PROTEIN / REPLICATION-DNA complex
Function / homology
Function and homology information


DNA endonuclease activity, producing 5'-phosphomonoesters / rolling circle single-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / nucleotidyltransferase activity / helicase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / nucleotide binding / host cell nucleus / structural molecule activity ...DNA endonuclease activity, producing 5'-phosphomonoesters / rolling circle single-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / nucleotidyltransferase activity / helicase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / nucleotide binding / host cell nucleus / structural molecule activity / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Geminivirus AL1, replication-associated protein / Geminivirus AL1 replication-associated protein, CLV type / Geminivirus AL1 replication-associated protein, central domain / Geminivirus Rep catalytic domain / Geminivirus rep protein central domain / : / CRESS-DNA virus replication initiator protein (Rep) endonuclease domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / DNA / Replication-associated protein / Replication-associated protein
Similarity search - Component
Biological speciesWheat dwarf virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.612 Å
AuthorsTompkins, K. / Litzau, L.A. / Pornschloegl, L. / Nelson, A.T. / Evans III, R.L. / Gordon, W.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM119483 United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering.
Authors: Tompkins, K.J. / Houtti, M. / Litzau, L.A. / Aird, E.J. / Everett, B.A. / Nelson, A.T. / Pornschloegl, L. / Limon-Swanson, L.K. / Evans, R.L. / Evans, K. / Shi, K. / Aihara, H. / Gordon, W.R.
History
DepositionApr 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: 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
Revision 1.2Oct 18, 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: Replication-associated protein
C: DNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*C)-3')
F: DNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*C)-3')
D: Replication-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6587
Polymers36,4934
Non-polymers1653
Water905
1
A: Replication-associated protein
C: DNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3564
Polymers18,2462
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-12 kcal/mol
Surface area6820 Å2
MethodPISA
2
F: DNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*C)-3')
D: Replication-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3013
Polymers18,2462
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-11 kcal/mol
Surface area6370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.626, 50.626, 241.977
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Replication-associated protein / Rep


Mass: 15836.812 Da / Num. of mol.: 2 / Mutation: Y106F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wheat dwarf virus / Gene: rep / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0F6N3D1, UniProt: Q67622*PLUS, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: DNA chain DNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*C)-3')


Mass: 2409.630 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Wheat dwarf virus
#3: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.44 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% w/v PEG 8000, 0.1 M sodium cocadylate, pH 6.5, 0.2M zinc acetate, 25% glycerol

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.542 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.612→28.55 Å / Num. obs: 9674 / % possible obs: 93.29 % / Redundancy: 1.6 % / Biso Wilson estimate: 53.18 Å2 / CC1/2: 0.987 / CC star: 0.997 / Rpim(I) all: 0.071 / Rrim(I) all: 0.112 / Net I/σ(I): 7.7
Reflection shellResolution: 2.612→2.705 Å / Mean I/σ(I) obs: 2.27 / Num. unique obs: 876 / CC1/2: 0.702 / CC star: 0.908 / Rpim(I) all: 0.378 / Rrim(I) all: 0.609 / % possible all: 87.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6q1m

6q1m


Resolution: 2.612→28.55 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2435 805 5.08 %
Rwork0.1879 15051 -
obs0.1907 9674 86.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.39 Å2 / Biso mean: 47.1581 Å2 / Biso min: 25.85 Å2
Refinement stepCycle: final / Resolution: 2.612→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 320 3 5 2106
Biso mean--42.2 34.09 -
Num. residues----245
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.61-2.780.33591170.29312394251182
2.78-2.990.33911210.23832401252283
2.99-3.290.28381260.2492365249183
3.29-3.760.27141280.19022452258084
3.76-4.740.19541470.15572654280192
4.74-28.780.21991660.16272785295197

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