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- PDB-4or6: Structure of Influenza B PB2 cap-binding domain with Q325F mutati... -

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Basic information

Entry
Database: PDB / ID: 4or6
TitleStructure of Influenza B PB2 cap-binding domain with Q325F mutation complex with GDP
ComponentsPolymerase basic protein 2
KeywordsVIRAL PROTEIN / cap binding
Function / homology: / Influenza RNA polymerase PB2 CAP binding domain / host cell mitochondrion / GUANOSINE-5'-DIPHOSPHATE / Polymerase basic protein 2
Function and homology information
Biological speciesinfluenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.293 Å
AuthorsLiu, Y. / Fan, J. / Zheng, X.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The crystal structure of the PB2 cap-binding domain of influenza B virus reveals a novel cap recognition mechanism.
Authors: Liu, Y. / Yang, Y. / Fan, J. / He, R. / Luo, M. / Zheng, X.
History
DepositionFeb 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Polymerase basic protein 2
B: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1464
Polymers39,2592
Non-polymers8862
Water2,846158
1
A: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0732
Polymers19,6301
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0732
Polymers19,6301
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.974, 90.151, 95.706
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Polymerase basic protein 2


Mass: 19629.664 Da / Num. of mol.: 2 / Fragment: cap-binding domain / Mutation: Q325F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) influenza B virus / Strain: B/Jiangxi/BV/2006 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): bl21 (DE3) / References: UniProt: A0A0J9X1Y8*PLUS
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE IS FROM INFLUENZA B VIRUS (B/JIANGXI/BV/2006) WHICH WAS NOT SUBMITTED IN UNP. ...THIS SEQUENCE IS FROM INFLUENZA B VIRUS (B/JIANGXI/BV/2006) WHICH WAS NOT SUBMITTED IN UNP. RESIUDES 316-319 ARE THE EXPRESSION TAG. RESIDUE 325 REPRESENTS MUTATION Q325F.

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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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 3350, 0.15M DL-Malic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2013
RadiationMonochromator: Crystallogic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. all: 17196 / Num. obs: 17179 / % possible obs: 99.9 % / Observed criterion σ(I): 3.8 / Redundancy: 9.3 % / Biso Wilson estimate: 23.52 Å2
Reflection shellResolution: 2.29→2.36 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OR4

4or4


Resolution: 2.293→30.134 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.895 / SU ML: 0.27 / σ(F): 0.72 / Phase error: 22.94 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2457 865 5.08 %
Rwork0.1848 --
obs0.1878 17022 98.28 %
all-16440 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.764 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.293→30.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2648 0 56 158 2862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022792
X-RAY DIFFRACTIONf_angle_d0.6143746
X-RAY DIFFRACTIONf_dihedral_angle_d15.4061098
X-RAY DIFFRACTIONf_chiral_restr0.025386
X-RAY DIFFRACTIONf_plane_restr0.001478
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.293-2.43660.30991370.2168251193
2.4366-2.62470.2691590.2137264499
2.6247-2.88860.30811360.2129268899
2.8886-3.30620.25671380.1895272899
3.3062-4.16370.20471550.1604271599
4.1637-30.13690.22141400.1717287199

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