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- PDB-3wrn: Minute virus of mice non-structural protein-1N-terminal nuclease ... -

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Basic information

Entry
Database: PDB / ID: 3wrn
TitleMinute virus of mice non-structural protein-1N-terminal nuclease domain reveals a unique Zn2+ coordination in the active site pocket and shows a novel mode of DNA recognition at the origin of replication
ComponentsNon-capsid protein NS-1
KeywordsREPLICATION / Nuclease activity / Single and double stranded DNA binding / nicking protein
Function / homology
Function and homology information


rolling hairpin viral DNA replication / symbiont-mediated arrest of host cell cycle during G2/M transition / symbiont-mediated perturbation of host transcription / symbiont-mediated perturbation of host apoptosis / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / helicase activity / endonuclease activity / DNA helicase / DNA replication ...rolling hairpin viral DNA replication / symbiont-mediated arrest of host cell cycle during G2/M transition / symbiont-mediated perturbation of host transcription / symbiont-mediated perturbation of host apoptosis / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / helicase activity / endonuclease activity / DNA helicase / DNA replication / host cell nucleus / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Parvovirus non-structural protein 1, N-terminal / Parvovirus non-structural protein 1, C-terminal / Parvovirus non-structural protein 1, C-terminal / Parvovirus non-structural protein 1 / : / Parvovirus (PV) NS1 nuclease (NS1-Nuc) domain profile. / Parvovirus non-structural protein 1, helicase domain / Parvovirus non-structural protein NS1 / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Initiator protein NS1
Similarity search - Component
Biological speciesMurine minute virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.52 Å
AuthorsTewary, S.K. / Zhao, H. / Tang, L.
CitationJournal: Virology / Year: 2014
Title: Structures of minute virus of mice replication initiator protein N-terminal domain: Insights into DNA nicking and origin binding.
Authors: Tewary, S.K. / Liang, L. / Lin, Z. / Lynn, A. / Cotmore, S.F. / Tattersall, P. / Zhao, H. / Tang, L.
History
DepositionFeb 27, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-capsid protein NS-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4554
Polymers32,3431
Non-polymers1113
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.790, 121.430, 41.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Non-capsid protein NS-1 / NCVP1 / Non-structural protein NS1


Mass: 32343.402 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine minute virus / Strain: MVM prototype / Gene: NS1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3(834) / References: UniProt: P03134
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 2.8M sodium formate, 100mM sodium acetate trihydrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2014 / Details: Mirrors-Rh coated
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionHighest resolution: 1.52 Å / Num. obs: 44412

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Processing

Software
NameVersionClassification
SOLVEphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.52→32.328 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 20.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 2228 5.02 %Random
Rwork0.1683 ---
obs0.1699 38182 98.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→32.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 3 182 2259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062130
X-RAY DIFFRACTIONf_angle_d0.9212878
X-RAY DIFFRACTIONf_dihedral_angle_d13.513773
X-RAY DIFFRACTIONf_chiral_restr0.037297
X-RAY DIFFRACTIONf_plane_restr0.004360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.52-1.55310.3251430.2816256597
1.5531-1.58920.24941470.2343258999
1.5892-1.62890.2231180.2119264799
1.6289-1.6730.27081290.2075259698
1.673-1.72220.2221430.2002259498
1.7222-1.77780.23131460.1969259899
1.7778-1.84130.23161450.1887261599
1.8413-1.9150.21461360.1891260898
1.915-2.00220.18261240.1777262499
2.0022-2.10770.1951370.184260197
2.1077-2.23970.20441500.1635261699
2.2397-2.41260.1961270.1708268199
2.4126-2.65530.18611370.18192667100
2.6553-3.03930.23181330.1803268098
3.0393-3.82820.18011560.1515268598
3.8282-32.33530.17911570.1362281898
Refinement TLS params.Method: refined / Origin x: 5.012 Å / Origin y: 42.8221 Å / Origin z: 20.7649 Å
111213212223313233
T0.1529 Å20.0095 Å2-0.007 Å2-0.0916 Å2-0.0374 Å2--0.2149 Å2
L1.58 °20.5715 °2-0.301 °2-2.1571 °2-0.5648 °2--1.2525 °2
S0.0376 Å °-0.0029 Å °0.0255 Å °-0.0044 Å °0.0015 Å °-0.0662 Å °0.0109 Å °0.0157 Å °-0.0309 Å °
Refinement TLS groupSelection details: CHAIN A

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