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- PDB-4oro: Structure of Influenza B PB2 cap-binding domain complex with GDP -

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Basic information

Entry
Database: PDB / ID: 4oro
TitleStructure of Influenza B PB2 cap-binding domain complex with GDP
ComponentsPolymerase PB2
KeywordsVIRAL PROTEIN / cap binding
Function / homology: / Influenza RNA polymerase PB2 CAP binding domain / host cell mitochondrion / GUANOSINE-5'-DIPHOSPHATE / Polymerase PB2
Function and homology information
Biological speciesInfluenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLiu, Y. / Zheng, X.
CitationJournal: to be published
Title: Structure of Influenza B PB2 cap-binding domain complex with GDP
Authors: Liu, Y. / Zheng, X.
History
DepositionFeb 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 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 PB2
B: Polymerase PB2
C: Polymerase PB2
D: Polymerase PB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2158
Polymers78,4424
Non-polymers1,7734
Water4,017223
1
A: Polymerase PB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0542
Polymers19,6111
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polymerase PB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0542
Polymers19,6111
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Polymerase PB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0542
Polymers19,6111
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Polymerase PB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0542
Polymers19,6111
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.420, 42.771, 118.414
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
Polymerase PB2 / Polymerase basic protein 2


Mass: 19610.619 Da / Num. of mol.: 4 / Fragment: cap-binding domain
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: A0A0M3KKU8*PLUS
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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.

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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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 20% PEG 3350, 0.2M potassium sodium tartrate, 0.1M Bis-Tris, pH 6.4, 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: Jan 1, 2014
RadiationMonochromator: Crystallogic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 33156 / Num. obs: 32029 / % possible obs: 96.6 % / Observed criterion σ(I): 3.5 / Redundancy: 4.3 %
Reflection shellResolution: 2.4→2.44 Å / % possible all: 96.3

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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: 4OR4

4or4


Resolution: 2.4→39.47 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.892 / SU B: 8.339 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.449 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26982 1625 5.1 %RANDOM
Rwork0.19906 ---
obs0.20271 30304 95.88 %-
all-31606 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.745 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.01 Å2
2--0 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5484 0 112 223 5819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0225684
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9871.9867600
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7055672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33523.662284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.317151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6521556
X-RAY DIFFRACTIONr_chiral_restr0.1250.2788
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024192
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_it0.9471.53320
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.84325309
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.12832364
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1274.52291
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: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 104 -
Rwork0.211 2060 -
obs--89.53 %

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