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- PDB-7szy: High-resolution structure of the nuclease domain from the main re... -

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Basic information

Entry
Database: PDB / ID: 7szy
TitleHigh-resolution structure of the nuclease domain from the main replication protein NS1 of Human Parvovirus B19
ComponentsNS1 protein
KeywordsVIRAL PROTEIN / nuclease domain / viral origin of replication binding domain / parvovirus / double-stranded DNA binding / DNA nicking
Function / homology
Function and homology information


viral genome replication / endonuclease activity / DNA replication / host cell nucleus / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Rep protein catalytic-like / Rep protein catalytic domain like / Replication Protein E1; Chain: A, - #20 / : / Parvovirus (PV) NS1 nuclease (NS1-Nuc) domain profile. / Parvovirus non-structural protein 1, helicase domain / Parvovirus non-structural protein NS1 / Replication Protein E1; Chain: A, / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. ...Rep protein catalytic-like / Rep protein catalytic domain like / Replication Protein E1; Chain: A, - #20 / : / Parvovirus (PV) NS1 nuclease (NS1-Nuc) domain profile. / Parvovirus non-structural protein 1, helicase domain / Parvovirus non-structural protein NS1 / Replication Protein E1; Chain: A, / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / NS1 protein
Similarity search - Component
Biological speciesHuman parvovirus B19
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHorton, N.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: J.Virol. / Year: 2022
Title: High-Resolution Structure of the Nuclease Domain of the Human Parvovirus B19 Main Replication Protein NS1.
Authors: Sanchez, J.L. / Ghadirian, N. / Horton, N.C.
History
DepositionNov 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 25, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 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: NS1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0772
Polymers19,8851
Non-polymers1921
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.060, 49.100, 74.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein NS1 protein


Mass: 19884.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human parvovirus B19 / Production host: Escherichia coli (E. coli) / References: UniProt: A3F778
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 15% PEG 3350 0.1M sodium citrate pH 4.5 0.1M NaCl 0.1M LiCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.4→45.06 Å / Num. obs: 6799 / % possible obs: 98.44 % / Redundancy: 2 % / Biso Wilson estimate: 28.31 Å2 / CC1/2: 0.981 / CC star: 0.995 / Rmerge(I) obs: 0.1022 / Rpim(I) all: 0.1022 / Rrim(I) all: 0.1446 / Net I/σ(I): 7.21
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5331 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 665 / CC1/2: 0.385 / CC star: 0.745 / Rpim(I) all: 0.5331 / Rrim(I) all: 0.7539 / % possible all: 98.66

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6USM

6usm


Resolution: 2.4→45.06 Å / SU ML: 0.2778 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1193
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2571 333 4.9 %Random Selection
Rwork0.1981 6464 --
obs0.2009 6797 98.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.11 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 13 89 1439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271382
X-RAY DIFFRACTIONf_angle_d0.61291881
X-RAY DIFFRACTIONf_chiral_restr0.0411210
X-RAY DIFFRACTIONf_plane_restr0.0028239
X-RAY DIFFRACTIONf_dihedral_angle_d19.4832473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-3.020.29691660.23913159X-RAY DIFFRACTION98.34
3.02-45.060.23791670.18053305X-RAY DIFFRACTION98.52

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