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

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Basic information

Entry
Database: PDB / ID: 3wro
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 / DNA helicase / endonuclease activity / 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 / DNA helicase / endonuclease activity / 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: 1.48 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.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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,3982
Polymers32,3431
Non-polymers551
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.240, 121.350, 41.750
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


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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.24 Å3/Da / Density % sol: 45.13 %
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: 1.48 Å / Num. obs: 48534

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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: 1.48→32.499 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 19.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1955 2383 4.91 %
Rwork0.1713 --
obs0.1725 48534 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.48→32.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 1 170 2245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052130
X-RAY DIFFRACTIONf_angle_d0.9382878
X-RAY DIFFRACTIONf_dihedral_angle_d13.43773
X-RAY DIFFRACTIONf_chiral_restr0.067297
X-RAY DIFFRACTIONf_plane_restr0.004360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.48-1.51020.30641310.2699270299
1.5102-1.54310.26311530.2436268998
1.5431-1.57890.24431240.2231267099
1.5789-1.61840.22211430.2049266798
1.6184-1.66220.20791500.2073266698
1.6622-1.71110.2161300.1919269199
1.7111-1.76630.20931190.19273299
1.7663-1.82940.20711300.1912272499
1.8294-1.90270.20631440.1837270399
1.9027-1.98930.19741320.1851270298
1.9893-2.09410.19511320.1758271398
2.0941-2.22530.20651490.17270899
2.2253-2.39710.20631330.1763273199
2.3971-2.63820.22291430.1855274698
2.6382-3.01970.18971540.1821269397
3.0197-3.80360.16291560.1549276598
3.8036-32.50650.18461600.1396284996
Refinement TLS params.Method: refined / Origin x: 5.021 Å / Origin y: 42.7894 Å / Origin z: 20.7811 Å
111213212223313233
T0.098 Å20.008 Å2-0.0123 Å2-0.1056 Å2-0.0421 Å2--0.1021 Å2
L1.873 °20.657 °2-0.6811 °2-2.737 °2-0.9831 °2--1.8182 °2
S0.0599 Å °-0.0223 Å °0.0277 Å °-0.0018 Å °-0.0148 Å °-0.085 Å °-0.0262 Å °0.0236 Å °-0.0372 Å °
Refinement TLS groupSelection details: CHAIN A

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