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- PDB-7kik: Wheat dwarf virus Rep domain circular permutation complexed with ... -

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Basic information

Entry
Database: PDB / ID: 7kik
TitleWheat dwarf virus Rep domain circular permutation complexed with a single-stranded DNA 10-mer comprising the cleavage site and Mn2+
Components
  • DNA (5'-D(*TP*AP*AP*TP*AP*TP*TP*AP*CP*C)-3')
  • Replication-associated protein
KeywordsREPLICATION/DNA / HUH-tag / HUH motif / Rep domain / viral protein / single stranded DNA / ssDNA / ssDNA binding / REPLICATION / DNA BINDING PROTEIN / REPLICATION-DNA complex
Function / homology
Function and homology information


endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / DNA replication / host cell nucleus / structural molecule activity / DNA binding / metal ion binding
Similarity search - Function
Geminivirus AL1 replication-associated protein, catalytic domain / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / DNA / Replication-associated protein
Similarity search - Component
Biological speciesWheat dwarf virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsTompkins, K.J. / Gordon, W.R. / Shi, K. / Litzau, L.A.
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: Mbio / Year: 2023
Title: Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases.
Authors: Smiley, A.T. / Tompkins, K.J. / Pawlak, M.R. / Krueger, A.J. / Evans 3rd, R.L. / Shi, K. / Aihara, H. / Gordon, W.R.
History
DepositionOct 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)18,6523
Polymers18,5982
Non-polymers551
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-15 kcal/mol
Surface area7390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.252, 94.252, 50.107
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Replication-associated protein / Rep


Mass: 15594.540 Da / Num. of mol.: 1 / Mutation: Y22F
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: A0A0F6N442, 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.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1 M Bis-tris, pH 6.2, 10% polyethylene glycol, 20% glycerol added to drop

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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: Sep 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.73→66.65 Å / Num. obs: 22917 / % possible obs: 99.09 % / Redundancy: 3 % / Biso Wilson estimate: 28.16 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.07361 / Rpim(I) all: 0.05003 / Rrim(I) all: 0.0894 / Net I/σ(I): 14.14
Reflection shellResolution: 1.73→1.792 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.7564 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2283 / CC1/2: 0.994 / CC star: 0.923 / Rpim(I) all: 0.5207 / Rrim(I) all: 0.9219 / % possible all: 99.04

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WE0

6we0


Resolution: 1.73→66.65 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1874 1092 4.77 %
Rwork0.1559 21806 -
obs0.1574 22883 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.14 Å2 / Biso mean: 33.8815 Å2 / Biso min: 18.16 Å2
Refinement stepCycle: final / Resolution: 1.73→66.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 182 1 162 1320
Biso mean--29.19 47 -
Num. residues----131
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.73-1.810.54661260.37012684281098
1.81-1.90.3521240.2552719284399
1.9-2.020.23681520.19192707285999
2.02-2.180.21331410.15432707284899
2.18-2.40.20641490.16982707285699
2.4-2.740.19271340.149727472881100
2.75-3.460.16851140.14742764287899
3.46-66.650.14531520.12982771292398

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