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- PDB-4z5v: Crystal Structure of MHV ns2 PDE Domain -

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Basic information

Entry
Database: PDB / ID: 4z5v
TitleCrystal Structure of MHV ns2 PDE Domain
ComponentsNon-structural protein 2a
KeywordsVIRAL PROTEIN / Murine hepatitis virus / ns2 protein / Phosphodiesterase
Function / homologyCoronavirus NS2A / NS2A-like / Coronavirus NS2A protein / host cell cytoplasm / Non-structural protein 2a
Function and homology information
Biological speciesMurine coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.049 Å
AuthorsSui, B.K. / Huang, J.H. / Peng, G.Q. / Zhao, L.
CitationJournal: J.Gen.Virol. / Year: 2016
Title: Crystal structure of the mouse hepatitis virus ns2 phosphodiesterase domain that antagonizes RNase L activation
Authors: Sui, B.K. / Huang, J.H. / Jha, B.K. / Yin, P. / Zhou, M. / Fu, Z.F. / Silverman, R.H. / Weiss, S.R. / Peng, G.Q. / Zhao, L.
History
DepositionApr 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-structural protein 2a
B: Non-structural protein 2a


Theoretical massNumber of molelcules
Total (without water)48,2802
Polymers48,2802
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-4 kcal/mol
Surface area17270 Å2
Unit cell
Length a, b, c (Å)101.042, 101.042, 165.806
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Non-structural protein 2a / ns2a / 30 kDa accessory protein / 30 kDa non-structural protein / ns2 / p30


Mass: 24139.852 Da / Num. of mol.: 2 / Fragment: UNP residues 2-199
Source method: isolated from a genetically manipulated source
Details: phosphodiesterase / Source: (gene. exp.) Murine coronavirus (strain A59) / Strain: A59 / Gene: 2a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P19738
Has protein modificationY

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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: 4.4 Å3/Da / Density % sol: 72.9 %
Description: the entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 16% PEG3350, 0.1M succinic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. all: 32650 / Num. obs: 31292 / % possible obs: 99.9 % / Redundancy: 8.6 % / Biso Wilson estimate: 92.19 Å2 / Rpim(I) all: 0.023 / Rrim(I) all: 0.089 / Χ2: 1.277 / Net I/av σ(I): 32.926 / Net I/σ(I): 20.6 / Num. measured all: 274550
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1752 / CC1/2: 0.899 / Rpim(I) all: 0.223 / Rrim(I) all: 0.903 / Χ2: 1.312 / Rejects: 0 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data processing
PHENIX1.8.2-1309phasing
RefinementMethod to determine structure: SAD / Resolution: 3.049→48.489 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.76 / Stereochemistry target values: ML
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.266 3124 10 %
Rwork0.2262 --
obs0.2301 31252 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.37 Å2
Refinement stepCycle: LAST / Resolution: 3.049→48.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2511 0 0 0 2511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012566
X-RAY DIFFRACTIONf_angle_d1.2523457
X-RAY DIFFRACTIONf_dihedral_angle_d17.748954
X-RAY DIFFRACTIONf_chiral_restr0.086374
X-RAY DIFFRACTIONf_plane_restr0.005448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0493-3.09690.3471390.31231264X-RAY DIFFRACTION99
3.0969-3.14770.35331390.30331287X-RAY DIFFRACTION100
3.1477-3.2020.31241430.28411266X-RAY DIFFRACTION100
3.202-3.26020.35071420.28431315X-RAY DIFFRACTION100
3.2602-3.32290.35761390.27291271X-RAY DIFFRACTION100
3.3229-3.39070.32721390.22591284X-RAY DIFFRACTION100
3.3907-3.46440.23521430.23061277X-RAY DIFFRACTION100
3.4644-3.5450.29311420.23911266X-RAY DIFFRACTION100
3.545-3.63360.28611470.24281288X-RAY DIFFRACTION100
3.6336-3.73180.2661460.24171295X-RAY DIFFRACTION100
3.7318-3.84160.25231380.23391265X-RAY DIFFRACTION100
3.8416-3.96550.23731400.241284X-RAY DIFFRACTION100
3.9655-4.10720.29851390.22751272X-RAY DIFFRACTION100
4.1072-4.27150.26061390.21461266X-RAY DIFFRACTION100
4.2715-4.46580.20991380.19831295X-RAY DIFFRACTION100
4.4658-4.70110.21681420.17031273X-RAY DIFFRACTION100
4.7011-4.99530.23861460.17571291X-RAY DIFFRACTION100
4.9953-5.38050.19541470.19671268X-RAY DIFFRACTION100
5.3805-5.92120.26421420.22881288X-RAY DIFFRACTION100
5.9212-6.7760.2931420.23731280X-RAY DIFFRACTION100
6.776-8.52940.25851480.25141267X-RAY DIFFRACTION100
8.5294-48.4950.2951440.22961266X-RAY DIFFRACTION98

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