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

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Basic information

Entry
Database: PDB / ID: 3wrq
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 perturbation of host transcription / symbiont-mediated arrest of host cell cycle during G2/M transition / 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 perturbation of host transcription / symbiont-mediated arrest of host cell cycle during G2/M transition / 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
NICKEL (II) ION / Initiator protein NS1
Similarity search - Component
Biological speciesMurine minute virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.53 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,4022
Polymers32,3431
Non-polymers591
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.280, 121.260, 41.650
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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 44.99 %
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: 1.53 Å / Num. obs: 43991

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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: 1.53→30.315 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 20.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1992 2205 5.01 %
Rwork0.1739 --
obs0.1752 43991 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.53→30.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 1 196 2271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062130
X-RAY DIFFRACTIONf_angle_d0.9272878
X-RAY DIFFRACTIONf_dihedral_angle_d13.11773
X-RAY DIFFRACTIONf_chiral_restr0.04297
X-RAY DIFFRACTIONf_plane_restr0.005360
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 (%)
1.53-1.56330.25451500.2495251096
1.5633-1.59960.25431420.2252601100
1.5996-1.63960.23351130.2147260999
1.6396-1.6840.24871340.1953260299
1.684-1.73350.19561430.1964258799
1.7335-1.78950.23941390.199253198
1.7895-1.85340.23221490.1873256098
1.8534-1.92760.21641350.1825261099
1.9276-2.01530.20791210.1716263399
2.0153-2.12150.18941290.1698262099
2.1215-2.25440.21521510.1652257598
2.2544-2.42840.18961270.175259797
2.4284-2.67270.19081330.1832263999
2.6727-3.05910.22161330.1866269599
3.0591-3.85290.17761540.1625262997
3.8529-30.32090.18091520.1532278898
Refinement TLS params.Method: refined / Origin x: 4.869 Å / Origin y: 42.7319 Å / Origin z: 20.7703 Å
111213212223313233
T0.1324 Å20.0098 Å2-0.0078 Å2-0.0933 Å2-0.041 Å2--0.1851 Å2
L1.6445 °20.3867 °2-0.3595 °2-2.1497 °2-0.6838 °2--1.5025 °2
S0.0574 Å °-0.0035 Å °0.0597 Å °0.0123 Å °0.0017 Å °-0.0702 Å °-0.0642 Å °0.0053 Å °-0.0395 Å °
Refinement TLS groupSelection details: CHAIN A

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