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

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Basic information

Entry
Database: PDB / ID: 7kij
TitleMuscovy duck circovirus Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site
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


nucleotidyltransferase activity / endonuclease activity / DNA replication / RNA helicase activity / nucleotide binding / host cell nucleus / DNA binding / RNA binding / metal ion binding
Similarity search - Function
Putative viral replication protein / : / CRESS-DNA virus replication initiator protein (Rep) endonuclease domain profile. / 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: 1.69 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
C: ATP-dependent helicase Rep
D: DNA (5'-D(*TP*AP*TP*TP*AP*TP*TP*AP*CP*C)-3')
A: ATP-dependent helicase Rep
B: DNA (5'-D(*TP*AP*TP*TP*AP*TP*TP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,29110
Polymers30,7594
Non-polymers5316
Water5,062281
1
C: ATP-dependent helicase Rep
D: DNA (5'-D(*TP*AP*TP*TP*AP*TP*TP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7606
Polymers15,3802
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-24 kcal/mol
Surface area6450 Å2
MethodPISA
2
A: ATP-dependent helicase Rep
B: DNA (5'-D(*TP*AP*TP*TP*AP*TP*TP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5314
Polymers15,3802
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-38 kcal/mol
Surface area6110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.986, 102.986, 138.294
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11B-513-

HOH

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Components

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Protein / DNA chain , 2 types, 4 molecules CADB

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


Mass: 12385.729 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Source: (synth.) Muscovy duck circovirus

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Non-polymers , 4 types, 287 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 3.44 Å3/Da / Density % sol: 64.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate, pH 4.8, 2.2M ammonium sulfate, 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: 1.69→54.65 Å / Num. obs: 48935 / % possible obs: 99.84 % / Redundancy: 8.7 % / Biso Wilson estimate: 28.27 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.03628 / Rpim(I) all: 0.01275 / Rrim(I) all: 0.03856 / Net I/σ(I): 32.89
Reflection shellResolution: 1.69→1.751 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.8253 / Mean I/σ(I) obs: 2.28 / Num. unique obs: 4791 / CC1/2: 0.784 / CC star: 0.938 / Rpim(I) all: 0.2922 / Rrim(I) all: 0.8776 / % possible all: 99.69

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Processing

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

6wdz


Resolution: 1.69→54.65 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1946 2401 4.91 %
Rwork0.1706 46523 -
obs0.1718 48924 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.21 Å2 / Biso mean: 34.3287 Å2 / Biso min: 20.12 Å2
Refinement stepCycle: final / Resolution: 1.69→54.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1570 380 21 281 2252
Biso mean--61.27 46.66 -
Num. residues----218
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.69-1.720.40221410.334626772818100
1.72-1.760.31051550.297826492804100
1.76-1.80.26951450.254426912836100
1.8-1.850.24331330.228327012834100
1.85-1.90.22531530.206326822835100
1.9-1.950.21581170.183827132830100
1.95-2.020.22761470.165327042851100
2.02-2.090.19031260.15527122838100
2.09-2.170.18511470.151127012848100
2.17-2.270.18851240.146427412865100
2.27-2.390.1841320.156927412873100
2.39-2.540.19411260.162127352861100
2.54-2.740.20441420.172627472889100
2.74-3.010.18541530.17227652918100
3.01-3.450.19511460.166727862932100
3.45-4.340.15611580.143927992957100
4.35-54.650.19711560.18042979313599

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