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- PDB-5if2: Crystal structure of polymerase acid protein (PA) from Influenza ... -

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Basic information

Entry
Database: PDB / ID: 5if2
TitleCrystal structure of polymerase acid protein (PA) from Influenza A virus, WILSON-SMITH/1933 (H1N1) bound to fragment hit EBSI-576 (5,6-dichloro-1H-1,3-benzodiazol-2-yl)methanol
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / NIAID / structural genomics / fragment screening / STD NMR / flu / RdRp / polymerase / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


RNA polymerase activity / negative regulation of viral transcription / negative stranded viral RNA replication / negative regulation of viral genome replication / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / protein import into nucleus / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds ...RNA polymerase activity / negative regulation of viral transcription / negative stranded viral RNA replication / negative regulation of viral genome replication / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / protein import into nucleus / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA
Similarity search - Domain/homology
(5,6-dichloro-1H-benzimidazol-2-yl)methanol / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Fragment screening by STD NMR identifies novel site binders against influenza A virus polymerase PA
Authors: Pierce, P. / Muruthi, M.M. / Abendroth, J. / Moen, S.O. / Begley, D.W. / Davies, D.R. / Marathias, V.M. / Staker, B.L. / Myler, P.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionFeb 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4274
Polymers53,0971
Non-polymers3313
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-8 kcal/mol
Surface area19430 Å2
2
A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8558
Polymers106,1932
Non-polymers6616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area3960 Å2
ΔGint-26 kcal/mol
Surface area35790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.890, 68.890, 396.920
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Polymerase acidic protein / RNA-directed RNA polymerase subunit P2


Mass: 53096.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Wilson-Smith/1933 H1N1)
Strain: A/Wilson-Smith/1933 H1N1 / Gene: PA / Production host: Escherichia coli (E. coli) / References: UniProt: P15659
#2: Chemical ChemComp-6B1 / (5,6-dichloro-1H-benzimidazol-2-yl)methanol


Mass: 217.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6Cl2N2O
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 20 mg/mL protein against Morpheus screen condition H6 10% PEG 8000, 20% EG, 0.02 M each amino acid, 0.1 M MOPS/Hepes pH 7.5, unique puck ID pyl5-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 24630 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Biso Wilson estimate: 42.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Net I/σ(I): 19.45
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.35-2.410.5913.91100
2.41-2.480.4864.71100
2.48-2.550.4025.771100
2.55-2.630.3476.551100
2.63-2.710.2917.7199.9
2.71-2.810.2329.341100
2.81-2.910.17611.871100
2.91-3.030.14814.011100
3.03-3.170.11217.53199.9
3.17-3.320.09919.641100
3.32-3.50.07525.19199.9
3.5-3.720.06329.611100
3.72-3.970.05533.06199.9
3.97-4.290.04538.061100
4.29-4.70.04341.771100
4.7-5.250.04241.641100
5.25-6.070.04338.11100
6.07-7.430.03940.81100
7.43-10.510.03246.1199.8
10.51-44.3040.0344.69197.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→44.304 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 20.39
RfactorNum. reflection% reflection
Rfree0.2159 1948 7.91 %
Rwork0.1756 --
obs0.1789 24625 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.73 Å2 / Biso mean: 49.1955 Å2 / Biso min: 16.07 Å2
Refinement stepCycle: final / Resolution: 2.35→44.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 18 129 3312
Biso mean--75.56 45.9 -
Num. residues----409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073278
X-RAY DIFFRACTIONf_angle_d0.7884443
X-RAY DIFFRACTIONf_chiral_restr0.044496
X-RAY DIFFRACTIONf_plane_restr0.005567
X-RAY DIFFRACTIONf_dihedral_angle_d15.881991
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3501-2.40890.27351390.212615561695
2.4089-2.4740.26641490.201115781727
2.474-2.54680.25261300.18515811711
2.5468-2.6290.23391250.176415691694
2.629-2.7230.23081130.174716141727
2.723-2.8320.20161260.182315771703
2.832-2.96080.2611370.184715881725
2.9608-3.11690.25221360.187716101746
3.1169-3.31210.23271390.180216081747
3.3121-3.56770.23231480.168115881736
3.5677-3.92660.17881510.16816191770
3.9266-4.49430.17341490.140716471796
4.4943-5.66050.17831620.162116881850
5.6605-44.31230.24741440.202218541998
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)
10.76810.57010.88232.1444-0.5572.6616-0.14280.110.0027-0.1691-0.09-0.0055-0.0137-0.3246-0.06340.33570.13550.08340.23720.08290.2749-14.8649-30.513849.6339
20.0263-0.01650.05340.8803-0.01471.0754-0.0619-0.245-0.25380.12390.08770.19490.3585-0.22380.00130.30810.09250.09030.22730.07250.3123-22.4253-43.469562.099
30.245-0.0710.28280.6832-0.07930.3321-0.039-0.0109-0.01190.1641-0.0774-0.1833-0.03560.04770.02410.36070.3260.10820.2230.11120.3492-14.6808-36.059165.8949
40.4644-0.10750.04781.3217-0.6381.6988-0.02930.05430.0657-0.06180.0556-0.0572-0.2244-0.22990.0090.27160.15580.07250.1830.0650.2129-19.4605-25.140751.2538
50.52450.2222-0.55110.73110.09280.66840.03030.27840.2085-0.1936-0.175-0.4362-0.60490.26240.0390.51060.00910.11120.39130.18650.4716-4.2219-16.060337.6798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 265 through 302 )A265 - 302
2X-RAY DIFFRACTION2chain 'A' and (resid 303 through 350 )A303 - 350
3X-RAY DIFFRACTION3chain 'A' and (resid 351 through 405 )A351 - 405
4X-RAY DIFFRACTION4chain 'A' and (resid 406 through 602 )A406 - 602
5X-RAY DIFFRACTION5chain 'A' and (resid 603 through 713 )A603 - 713

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