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- PDB-7kii: Muscovy duck circovirus Rep domain complexed with a single-strand... -

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Basic information

Entry
Database: PDB / ID: 7kii
TitleMuscovy duck circovirus Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site and Mn2+
Components
  • ATP-dependent helicase Rep
  • DNA (5'-D(*TP*AP*TP*TP*AP*TP*TP*AP*CP*C)-3')
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 / nucleotidyltransferase activity / DNA replication / RNA helicase activity / RNA binding
Similarity search - Function
Viral replication-associated protein, N-terminal / Putative viral replication protein / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / DNA / Replication-associated protein
Similarity search - Component
Biological speciesMuscovy duck circovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsTompkins, K.J. / Gordon, W.R. / Shi, K.
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

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent helicase Rep
C: DNA (5'-D(*TP*AP*TP*TP*AP*TP*TP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6116
Polymers15,3802
Non-polymers2314
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-38 kcal/mol
Surface area5990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.417, 66.343, 71.259
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-203-

CA

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Components

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Protein / DNA chain , 2 types, 2 molecules AC

#1: Protein ATP-dependent helicase Rep / RepP / Replication-associated protein


Mass: 12385.729 Da / Num. of mol.: 1 / Mutation: Y91F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Muscovy duck circovirus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D2JZX8
#2: DNA chain DNA (5'-D(*TP*AP*TP*TP*AP*TP*TP*AP*CP*C)-3')


Mass: 2993.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Muscovy duck circovirus

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Non-polymers , 4 types, 192 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.13 Å3/Da / Density % sol: 42.23 % / Description: orthorhombic, 200 x 200 x 100 microns
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1 M sodium acetate, pH 4.8, 20 mM Calcium chloride, 26% 2-methyl-2,4-pentanediol, 30% polyethylene glycol 200 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: 1.3→48.56 Å / Num. obs: 32195 / % possible obs: 98.42 % / Redundancy: 4.6 % / Biso Wilson estimate: 14.46 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05301 / Rpim(I) all: 0.0254 / Rrim(I) all: 0.05902 / Net I/σ(I): 12.24
Reflection shellResolution: 1.3→1.346 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.3681 / Mean I/σ(I) obs: 2.18 / Num. unique obs: 3197 / CC1/2: 0.943 / CC star: 0.985 / Rpim(I) all: 0.1961 / Rrim(I) all: 0.4191 / % possible all: 99.35

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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: 6WDZ

6wdz


Resolution: 1.3→48.56 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 23.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1843 1649 5.11 %
Rwork0.1492 30625 -
obs0.151 32141 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.22 Å2 / Biso mean: 23.1329 Å2 / Biso min: 10.85 Å2
Refinement stepCycle: final / Resolution: 1.3→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms806 198 8 188 1200
Biso mean--65.81 35.05 -
Num. residues----113
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.330.33681380.29072425256394
1.33-1.380.26451290.23352550267999
1.38-1.430.26531330.1982541267499
1.43-1.480.21851280.16792531265998
1.48-1.550.16421340.139125822716100
1.55-1.630.1761440.12682554269899
1.63-1.740.15531200.13112597271799
1.74-1.870.17461440.13742567271199
1.87-2.060.17311300.14162536266697
2.06-2.360.18611320.14762588272099
2.36-2.970.17511640.15912549271398
2.97-48.560.17741530.13592605275895

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