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- PDB-4r94: Structure of the nickase domain of NS1 from MVM complexed with ma... -

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Basic information

Entry
Database: PDB / ID: 4r94
TitleStructure of the nickase domain of NS1 from MVM complexed with magnesium
ComponentsNon-structural protein NS1
KeywordsREPLICATION / nickase domain / DNA binding / magnesium / nickase
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
Initiator protein NS1
Similarity search - Component
Biological speciesMurine minute virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.668 Å
AuthorsLiang, L. / 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
DepositionSep 3, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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-structural protein NS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0652
Polymers30,0411
Non-polymers241
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.016, 121.377, 41.581
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-structural protein NS1


Mass: 30040.857 Da / Num. of mol.: 1 / Fragment: nickase domain (UNP RESIDUES 1-255)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine minute virus / Strain: MVM prototype / Gene: NS1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P03134
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.39 Å3/Da / Density % sol: 48.64 %
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2014
Details: K-B pair of biomorph mirrors with two additional horizontally deflecting mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.668→50 Å / Num. obs: 34417 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 37.118
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 3.125 / Rsym value: 0.453 / % possible all: 95.9

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4PP4

4pp4


Resolution: 1.668→19.676 Å / SU ML: 0.15 / Isotropic thermal model: isotropic / Cross valid method: R-free / σ(F): 1.35 / Phase error: 21.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2123 1675 5 %random
Rwork0.1754 ---
all0.1773 34417 --
obs0.1773 33477 97.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.9 Å2
Refinement stepCycle: LAST / Resolution: 1.668→19.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 1 258 2333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072130
X-RAY DIFFRACTIONf_angle_d0.9712878
X-RAY DIFFRACTIONf_dihedral_angle_d13.751773
X-RAY DIFFRACTIONf_chiral_restr0.041297
X-RAY DIFFRACTIONf_plane_restr0.004360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6683-1.71740.26071350.212255496
1.7174-1.77280.27881340.2276256796
1.7728-1.83610.23031380.2138260096
1.8361-1.90960.20571360.1939259997
1.9096-1.99640.26341380.1903259897
1.9964-2.10150.23511370.1838261297
2.1015-2.2330.20861390.1814263598
2.233-2.40520.2111390.1837264797
2.4052-2.64670.23161410.1936267998
2.6467-3.02850.19551430.1959269398
3.0285-3.8110.20371440.1595276899
3.811-19.67770.1991510.1505285098

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