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- PDB-6we0: Wheat dwarf virus Rep domain complexed with a single-stranded DNA... -

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Basic information

Entry
Database: PDB / ID: 6we0
TitleWheat dwarf virus Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site
Components
  • DNA (5'-D(*TP*AP*AP*TP*AP*TP*TP*AP*CP*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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTompkins, K. / Litzau, L.A. / Shi, K. / Nelson, A. / Evans III, R.L. / Gordon, W.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM119483 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 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(*TP*AP*AP*TP*AP*TP*TP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8176
Polymers18,5982
Non-polymers2204
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Evidence that it folds correctly.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-25 kcal/mol
Surface area7050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.572, 50.010, 73.441
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 Replication-associated protein / Rep


Mass: 15594.540 Da / Num. of mol.: 1 / Mutation: Y106F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wheat dwarf virus / Gene: repA / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A7KQY4, UniProt: Q67622*PLUS, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: DNA chain DNA (5'-D(*TP*AP*AP*TP*AP*TP*TP*AP*CP*C)-3')


Mass: 3003.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Wheat dwarf virus
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→41.34 Å / Num. obs: 15366 / % possible obs: 95.23 % / Redundancy: 4.4 % / Biso Wilson estimate: 26.51 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.07455 / Rrim(I) all: 0.08357 / Net I/σ(I): 14.17
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.8513 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 1551 / CC1/2: 0.571 / CC star: 0.852 / Rrim(I) all: 0.9629 / % possible all: 98.54

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q1M

6q1m


Resolution: 1.8→41.34 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2162 818 5.32 %
Rwork0.1917 14546 -
obs0.193 15364 95.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.28 Å2 / Biso mean: 29.4686 Å2 / Biso min: 15.96 Å2
Refinement stepCycle: final / Resolution: 1.8→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms915 197 4 45 1161
Biso mean--29.97 35.82 -
Num. residues----129
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 (%)
1.8-1.910.29271440.25522433257798
1.91-2.060.27971290.21362461259098
2.06-2.270.20721400.18532451259198
2.27-2.60.24291290.18522435256496
2.6-3.270.22551320.19122384251693
3.27-41.340.18931440.1842382252689
Refinement TLS params.Method: refined / Origin x: 4.465 Å / Origin y: 14.5582 Å / Origin z: 10.5412 Å
111213212223313233
T0.201 Å20.0005 Å2-0.0087 Å2-0.2709 Å2-0.0025 Å2--0.1382 Å2
L1.1262 °20.5128 °2-0.4413 °2-1.4596 °2-0.3017 °2--1.8564 °2
S0.0104 Å °-0.0332 Å °0.0232 Å °-0.0193 Å °-0.0066 Å °-0.0805 Å °-0.018 Å °0.1442 Å °-0.021 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 126
2X-RAY DIFFRACTION1allB201
3X-RAY DIFFRACTION1allC299 - 308
4X-RAY DIFFRACTION1allS1 - 74
5X-RAY DIFFRACTION1allD202 - 204

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