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- PDB-4or4: Structure of Influenza B PB2 cap-binding domain with Q325F mutati... -

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Basic information

Entry
Database: PDB / ID: 4or4
TitleStructure of Influenza B PB2 cap-binding domain with Q325F mutation complex with m7GDP
ComponentsPolymerase basic protein 2
KeywordsVIRAL PROTEIN / cap binding
Function / homology: / Influenza RNA polymerase PB2 CAP binding domain / host cell mitochondrion / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / Polymerase basic protein 2
Function and homology information
Biological speciesinfluenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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 10, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Data collection / Database references / Category: citation / reflns
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _reflns.percent_possible_obs
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)40,1784
Polymers39,2592
Non-polymers9182
Water2,828157
1
A: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0892
Polymers19,6301
Non-polymers4591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0892
Polymers19,6301
Non-polymers4591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.936, 90.698, 95.774
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 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J9X1Y8*PLUS
#2: Chemical ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 459.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H19N5O11P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 3350, 0.2M ammonium acetate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2013
RadiationMonochromator: Crystallogic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 19377 / Num. obs: 19358 / % possible obs: 99.9 % / Observed criterion σ(I): 4.6 / Redundancy: 7.8 %
Reflection shellResolution: 2.2→2.24 Å / % possible all: 100

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Processing

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

4eqk


Resolution: 2.21→42.35 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.422 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24194 980 5.1 %RANDOM
Rwork0.17609 ---
obs0.17928 18247 99.08 %-
all-18416 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.764 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.21→42.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2656 0 58 157 2871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222821
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2131.9863790
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7785339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85623.716148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.01715555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5881528
X-RAY DIFFRACTIONr_chiral_restr0.1620.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022112
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.141.51626
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.14122609
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.62131195
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6774.51173
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.21→2.268 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 71 -
Rwork0.202 1260 -
obs--93.4 %

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