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- PDB-3r2v: Crystal structure of polymerase basic protein 2 E538-R753 from In... -

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Basic information

Entry
Database: PDB / ID: 3r2v
TitleCrystal structure of polymerase basic protein 2 E538-R753 from Influenza A virus A/Yokohama/2017/03 H3N2
ComponentsPB2 C-terminal subunit
KeywordsVIRAL PROTEIN / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Influenza / flu / polymerase basic / PB2 / H3N2 / H1N1 / H5N1 / virus / 2003 avian flu outbreak
Function / homology
Function and homology information


DNA-templated transcription / RNA binding
Similarity search - Function
Polymerase Basic Protein 2, C-terminal domain / PB2, C-terminal / : / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 6th domain / Influenza RNA polymerase PB2 CAP binding domain / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BORIC ACID / IODIDE ION / PB2 C-terminal subunit
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / SAD / molecular replacement / Resolution: 1.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: The Protein Maker: an automated system for high-throughput parallel purification.
Authors: Smith, E.R. / Begley, D.W. / Anderson, V. / Raymond, A.C. / Haffner, T.E. / Robinson, J.I. / Edwards, T.E. / Duncan, N. / Gerdts, C.J. / Mixon, M.B. / Nollert, P. / Staker, B.L. / Stewart, L.J.
History
DepositionMar 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 5, 2011Group: Database references
Revision 1.3Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: PB2 C-terminal subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,70113
Polymers24,2431
Non-polymers1,45812
Water3,801211
1
A: PB2 C-terminal subunit
hetero molecules

A: PB2 C-terminal subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,40126
Polymers48,4862
Non-polymers2,91624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area4810 Å2
ΔGint-16 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.810, 106.540, 33.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PB2 C-terminal subunit


Mass: 24242.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Yokohama/2017/03(H3N2) / Gene: PB2 / Production host: Escherichia coli (E. coli) / References: UniProt: F2Z275*PLUS
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH3O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 1.94 Å3/Da / Density % sol: 36.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: InvaB.07055.c.D17 PD00118 at 24.51 mg/mL against 0.1 M MIB pH 6.0, 25% PEG 1500, 100 mM NaI, crystal tracking ID 220930b6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionNumber: 247531 / Rmerge(I) obs: 0.032 / D res high: 1.3 Å / Num. obs: 86116 / % possible obs: 95.9
Diffraction reflection shellHighest resolution: 1.3 Å / Lowest resolution: 1.33 Å / Num. obs: 5535 / % possible obs: 83.4 % / Rmerge(I) obs: 0.291
ReflectionResolution: 1.3→50 Å / Num. all: 47417 / Num. obs: 46293 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 19.242 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.66
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 3.27 / Num. measured obs: 9189 / Num. unique all: 3441 / Num. unique obs: 2983 / % possible all: 86.7

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Phasing

Phasing
Method
SAD
molecular replacement
Phasing MADD res high: 1.3 Å / D res low: 29.47 Å / FOM : 0.787 / FOM acentric: 0.796 / FOM centric: 0.714 / Reflection: 46104 / Reflection acentric: 39756 / Reflection centric: 4582
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.78-29.470.6090.7810.4391104457
6.35-8.780.7470.8360.55325816484
5.23-6.350.7930.8550.65233923891
4.55-5.230.8580.8910.78438928291
4.08-4.550.8660.9140.67241632578
3.73-4.080.8660.9080.72346936485
3.45-3.730.8710.8950.79754242497
3.23-3.450.8470.8720.74856946298
3.05-3.230.8560.8860.71258148188
2.9-3.050.8560.8770.765652532103
2.76-2.90.8830.8850.88865254097
2.65-2.760.8650.8910.7269258092
2.54-2.650.8490.8790.6972360696
2.45-2.540.8640.880.76755640101
2.37-2.450.8480.8640.74175563895
2.29-2.370.860.8720.78580068696
2.23-2.290.8480.8750.876959981
2.16-2.230.8290.8490.714860728101
2.11-2.160.8340.8480.70584872891
2.05-2.110.8250.8410.709897765101
2-2.050.8330.8480.69991279197
1.96-20.8180.8280.72890579392
1.91-1.960.7860.80.71796981198
1.87-1.910.7870.7990.74293980888
1.84-1.870.8010.8090.73899488398
1.8-1.840.780.7870.675100188791
1.77-1.80.7770.7860.696100188894
1.74-1.770.7860.7920.7191063939106
1.71-1.740.8030.8080.721103493677
1.68-1.710.780.7820.736107795797
1.65-1.680.8060.8090.7621101974101
1.62-1.650.7790.7860.7031122992101
1.6-1.620.770.7740.706109398186
1.58-1.60.7670.7710.72111881044108
1.55-1.580.7570.760.6991143102684
1.53-1.550.7660.7730.6771160102996
1.51-1.530.7590.7630.7231203106699
1.49-1.510.7720.7790.7041212108193
1.47-1.490.7440.7470.7121213108183
1.45-1.470.7590.7660.67812271091103
1.44-1.450.750.7570.661265111994
1.42-1.440.750.7560.6731261112196
1.4-1.420.7450.7430.7331267111185
1.39-1.40.7390.7470.6221268111497
1.37-1.390.7370.7360.7261313114091
1.36-1.370.7480.7490.7321238110183
1.34-1.360.7530.7550.731237107091
1.33-1.340.7460.7470.7371234106484
1.31-1.330.7270.7310.7081217103883
1.3-1.310.7130.7140.62117199463
Phasing MRRfactor: 43.78 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.42 Å
Translation2.5 Å47.42 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
BOSdata collection
XDSdata reduction
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT
Starting model: PDB entry 2VY6

2vy6


Resolution: 1.3→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2141 / WRfactor Rwork: 0.1832 / Occupancy max: 1 / Occupancy min: 0.13 / FOM work R set: 0.8876 / SU B: 1.622 / SU ML: 0.032 / SU R Cruickshank DPI: 0.0583 / SU Rfree: 0.0554 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2094 2293 5 %RANDOM
Rwork0.1802 ---
obs0.1816 46148 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 47.78 Å2 / Biso mean: 17.4682 Å2 / Biso min: 6.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1477 0 15 211 1703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221535
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.972085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2935200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17523.27961
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75715268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5641512
X-RAY DIFFRACTIONr_chiral_restr0.080.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211137
X-RAY DIFFRACTIONr_mcbond_it1.2141.5967
X-RAY DIFFRACTIONr_mcangle_it1.98421561
X-RAY DIFFRACTIONr_scbond_it2.5923568
X-RAY DIFFRACTIONr_scangle_it3.8124.5519
X-RAY DIFFRACTIONr_rigid_bond_restr1.19931528
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 154 -
Rwork0.253 2817 -
all-2971 -
obs--86.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0062-0.46791.06691.4519-1.15672.46940.00290.013-0.0130.0802-0.0558-0.1009-0.12610.19820.05290.0281-0.024-0.0120.03070.00750.0106-4.152419.0191-8.0695
20.7014-0.03860.04350.6068-0.13030.64790.01220.086-0.0537-0.0372-0.0243-0.0048-0.01370.0660.01210.0203-0.0029-0.0010.0172-0.00490.0047-11.808413.7269-17.9354
30.3804-0.27450.1741.421-0.07780.55930.0076-0.0213-0.0730.05790.00220.0668-0.00470.0099-0.00980.0233-0.0049-0.00530.00470.00560.0163-14.64778.3486-11.2955
40.98030.12810.64620.2526-0.03840.6544-0.0068-0.12-0.05140.05620.04210.056-0.0933-0.0643-0.03530.04770.00010.00740.04330.02360.0266-17.63616.652-4.031
52.74280.1062-0.29261.6766-0.59031.54820.0187-0.0587-0.1620.03330.10340.2331-0.0396-0.2113-0.12210.00130.00530.00470.03280.02640.0462-36.357811.1484-13.1462
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A541 - 563
2X-RAY DIFFRACTION2A564 - 610
3X-RAY DIFFRACTION3A611 - 645
4X-RAY DIFFRACTION4A646 - 697
5X-RAY DIFFRACTION5A698 - 738

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