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- PDB-6q1m: Crystal structure of the wheat dwarf virus Rep domain -

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Basic information

Entry
Database: PDB / ID: 6q1m
TitleCrystal structure of the wheat dwarf virus Rep domain
ComponentsReplication-associated protein
KeywordsREPLICATION / HUH-tag / HUH motif / Rep domain / viral protein / single stranded DNA / ssDNA / ssDNA binding
Function / homology
Function and homology information


rolling circle single-stranded viral DNA replication / endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / nucleotidyltransferase activity / helicase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / host cell nucleus / structural molecule activity / DNA binding ...rolling circle single-stranded viral DNA replication / endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / nucleotidyltransferase activity / helicase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / host cell nucleus / structural molecule activity / DNA binding / ATP 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 / : / CRESS-DNA virus replication initiator protein (Rep) endonuclease domain profile. / Replication Protein E1; Chain: A, - #20 / Replication Protein E1; Chain: A, ...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 / : / CRESS-DNA virus replication initiator protein (Rep) endonuclease domain profile. / Replication Protein E1; Chain: A, - #20 / Replication Protein E1; Chain: A, / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Replication-associated protein / Replication-associated protein
Similarity search - Component
Biological speciesWheat dwarf virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsLitzau, L.A. / Everett, B.A. / Evans III, R.L. / Shi, K. / Tompkins, K. / 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: Acta Crystallogr.,Sect.F / Year: 2019
Title: Crystal structure of the Wheat dwarf virus Rep domain.
Authors: Everett, B.A. / Litzau, L.A. / Tompkins, K. / Shi, K. / Nelson, A. / Aihara, H. / Evans Iii, R.L. / Gordon, W.R.
History
DepositionAug 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 11, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9795
Polymers15,6111
Non-polymers3684
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.566, 49.566, 145.653
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw

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Components

#1: Protein Replication-associated protein / Rep


Mass: 15610.540 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wheat dwarf virus / Gene: repA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A7KQY4, UniProt: Q67622*PLUS, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.87 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Hepes

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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: Jun 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.24→49.92 Å / Num. obs: 52013 / % possible obs: 98.83 % / Redundancy: 6.5 % / Biso Wilson estimate: 14.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.028 / Rrim(I) all: 0.054 / Net I/σ(I): 18.8
Reflection shellResolution: 1.24→1.26 Å / Rmerge(I) obs: 0.952 / Num. unique obs: 2612 / CC1/2: 0.525

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: C-alphas of a trimmed pdb ID 1l2m

1l2m


Resolution: 1.24→46.92 Å / SU ML: 0.1121 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.7027
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1664 2557 4.92 %
Rwork0.1576 49409 -
obs0.1581 51966 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.54 Å2
Refinement stepCycle: LAST / Resolution: 1.24→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms962 0 24 109 1095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561122
X-RAY DIFFRACTIONf_angle_d0.86961541
X-RAY DIFFRACTIONf_chiral_restr0.0862169
X-RAY DIFFRACTIONf_plane_restr0.0062203
X-RAY DIFFRACTIONf_dihedral_angle_d12.9943620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.260.30611470.2662667X-RAY DIFFRACTION99.08
1.26-1.290.25891210.22932745X-RAY DIFFRACTION99.9
1.29-1.320.21231360.21392742X-RAY DIFFRACTION99.97
1.32-1.350.23241320.20172729X-RAY DIFFRACTION99.97
1.35-1.380.23191330.18612733X-RAY DIFFRACTION99.83
1.38-1.420.2111310.19222653X-RAY DIFFRACTION96.53
1.42-1.460.16991350.14782740X-RAY DIFFRACTION99.97
1.46-1.510.14731440.12342734X-RAY DIFFRACTION99.97
1.51-1.560.14191420.11752746X-RAY DIFFRACTION99.97
1.56-1.620.13881330.11562737X-RAY DIFFRACTION99.97
1.62-1.70.14271510.12132755X-RAY DIFFRACTION99.73
1.7-1.790.12221500.12692686X-RAY DIFFRACTION97.19
1.79-1.90.151500.13352768X-RAY DIFFRACTION99.76
1.9-2.050.16371490.13852765X-RAY DIFFRACTION99.62
2.05-2.250.17661440.1462796X-RAY DIFFRACTION99.22
2.25-2.580.16941380.16522734X-RAY DIFFRACTION96.57
2.58-3.250.17591450.16922808X-RAY DIFFRACTION97.81
3.25-46.920.15951760.17442871X-RAY DIFFRACTION94.6

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