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- PDB-7vg8: TYLCV Rep-DNA -

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Basic information

Entry
Database: PDB / ID: 7vg8
TitleTYLCV Rep-DNA
Components
  • DNA (5'-((DT)P*(DA)P*(DA)P*(DT)P*(DA)P*(DT)P*(DT)P*(DA)*(DC)P*)-3')
  • Replication-associated protein
KeywordsVIRAL PROTEIN / complex
Function / homology
Function and homology information


DNA endonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / nucleotidyltransferase activity / helicase activity / DNA replication / 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.
Similarity search - Domain/homology
: / DNA / Replication-associated protein
Similarity search - Component
Biological speciesTomato yellow leaf curl virus
Tomato yellow leaf curl virus-IL [MX: SLP:11]
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsZhang, S.Y. / Wang, C.N.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: structure of TYLCV Rep complexed with ssDNA
Authors: Zhang, S.Y. / Wang, C.N.
History
DepositionSep 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replication-associated protein
C: DNA (5'-((DT)P*(DA)P*(DA)P*(DT)P*(DA)P*(DT)P*(DT)P*(DA)*(DC)P*)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8633
Polymers15,8082
Non-polymers551
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-12 kcal/mol
Surface area6340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.976, 67.976, 40.433
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein Replication-associated protein / Rep


Mass: 13093.854 Da / Num. of mol.: 1 / Mutation: Y101F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tomato yellow leaf curl virus / Gene: AC1 / Production host: prokaryote coculture (bacteria)
References: UniProt: A0A286LJ32, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: DNA chain DNA (5'-((DT)P*(DA)P*(DA)P*(DT)P*(DA)P*(DT)P*(DT)P*(DA)*(DC)P*)-3')


Mass: 2713.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tomato yellow leaf curl virus-IL [MX: SLP:11]
Production host: DNA satellites (virus)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.95 Å3/Da / Density % sol: 58.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis-Tris pH 6.5, 28%w/v Polyethylene glyco monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.04→21.5 Å / Num. obs: 11179 / % possible obs: 93.96 % / Redundancy: 6 % / Biso Wilson estimate: 26.16 Å2 / CC1/2: 0.99 / Net I/σ(I): 13.1
Reflection shellResolution: 2.04→2.11 Å / Num. unique obs: 1028 / CC1/2: 0.72

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WE0

6we0


Resolution: 2.04→21.5 Å / SU ML: 0.2437 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.2802
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.267 529 4.73 %
Rwork0.2219 10650 -
obs0.2241 11179 94.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.12 Å2
Refinement stepCycle: LAST / Resolution: 2.04→21.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms892 178 1 139 1210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781113
X-RAY DIFFRACTIONf_angle_d0.99851534
X-RAY DIFFRACTIONf_chiral_restr0.056164
X-RAY DIFFRACTIONf_plane_restr0.0056167
X-RAY DIFFRACTIONf_dihedral_angle_d20.6219196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.250.45171220.38892446X-RAY DIFFRACTION87.14
2.25-2.570.32691430.28472568X-RAY DIFFRACTION92.21
2.57-3.240.26821310.2242763X-RAY DIFFRACTION97.67
3.24-21.50.20011330.1672873X-RAY DIFFRACTION99.11

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