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- PDB-7szx: Structure of the N-terminal nuclease and origin binding domain of... -

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Basic information

Entry
Database: PDB / ID: 7szx
TitleStructure of the N-terminal nuclease and origin binding domain of Human Parvovirus B19
ComponentsNS1 protein
KeywordsVIRAL PROTEIN / viral replication / DNA binding / DNA cleaving / DNA nicking / viral origin of replication
Function / homology
Function and homology information


viral genome replication / endonuclease activity / DNA replication / hydrolase activity / 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
Biological speciesHuman parvovirus B19
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsHorton, N.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
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 1.1Oct 12, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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
B: NS1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3622
Polymers25,3381
Non-polymers241
Water724
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)106.710, 106.710, 59.590
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein NS1 protein


Mass: 25337.631 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.87 Å3/Da / Density % sol: 68.18 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop
Details: 2.5 M sodium chloride 0.1 M Tris-HCl pH 7.0 200 mM MgCl2
PH range: 7

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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: May 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.5→50.08 Å / Num. obs: 5099 / % possible obs: 98.68 % / Redundancy: 2 % / Biso Wilson estimate: 91.66 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.07557 / Rpim(I) all: 0.07557 / Rrim(I) all: 0.1072 / Net I/σ(I): 5.37
Reflection shellResolution: 3.5→3.625 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4226 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 488 / CC1/2: 0.89 / CC star: 0.971 / Rpim(I) all: 0.4226 / Rrim(I) all: 0.5977 / % possible all: 97.41

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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: 3.5→50.08 Å / SU ML: 0.4762 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.9938
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2991 508 10.01 %
Rwork0.2622 4568 -
obs0.2658 5076 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.33 Å2
Refinement stepCycle: LAST / Resolution: 3.5→50.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1289 0 1 4 1294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00361320
X-RAY DIFFRACTIONf_angle_d0.86721801
X-RAY DIFFRACTIONf_chiral_restr0.0557203
X-RAY DIFFRACTIONf_plane_restr0.0057232
X-RAY DIFFRACTIONf_dihedral_angle_d14.0876437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.850.35671220.33631105X-RAY DIFFRACTION98
3.85-4.410.34011250.26261136X-RAY DIFFRACTION99.53
4.41-5.550.28771300.24681137X-RAY DIFFRACTION98.22
5.56-50.080.26541310.24641190X-RAY DIFFRACTION99.32

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