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- PDB-4awk: Influenza strain pH1N1 2009 polymerase subunit PA endonuclease in... -

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Basic information

Entry
Database: PDB / ID: 4awk
TitleInfluenza strain pH1N1 2009 polymerase subunit PA endonuclease in complex with diketo compound 1
ComponentsPOLYMERASE PA
KeywordsHYDROLASE / MANGANESE-DEPENDENT / PD...D-E...K SUPERFAMILY
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Restriction Endonuclease / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CI1 / : / Polymerase acidic protein
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKowalinski, E. / Zubieta, C. / Wolkerstorfer, A. / Szolar, O.H. / Ruigrok, R.W. / Cusack, S.
CitationJournal: Plos Pathog. / Year: 2012
Title: Structural Analysis of Specific Metal Chelating Inhibitor Binding to the Endonuclease Domain of Influenza Ph1N1 (2009) Polymerase.
Authors: Kowalinski, E. / Zubieta, C. / Wolkerstorfer, A. / Szolar, O.H. / Ruigrok, R.W. / Cusack, S.
History
DepositionJun 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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 PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1594
Polymers21,5721
Non-polymers5883
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.060, 75.060, 120.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein POLYMERASE PA


Mass: 21571.656 Da / Num. of mol.: 1 / Fragment: ENDONUCLEASE, RESIDUES 1-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/CALIFORNIA/04/2009(H1N1) / Description: SYNTHETIC GENE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C3W5S0
#2: Chemical ChemComp-CI1 / (2Z)-4-[(3S)-1-(benzylsulfonyl)-3-(4-chlorobenzyl)piperidin-3-yl]-2-hydroxy-4-oxobut-2-enoic acid


Mass: 477.958 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24ClNO6S
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsADDITIONAL MGSGMA AT N-TERMINUS. INTERNAL DELETION OF RESIDUES 52-64 AND REPLACEMENT WITH A GLYCINE

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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: 2.18 Å3/Da / Density % sol: 43.5 % / Description: NONE
Crystal growpH: 8.5 / Details: 25-30% PEG 4K, 0.1 M TRIS PH8.5, 0.2 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9724
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 16410 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 8.09 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.2
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.95 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W69

2w69


Resolution: 1.9→65.01 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.124 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23568 830 5.1 %RANDOM
Rwork0.2084 ---
obs0.20971 15580 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.398 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å20 Å2
2--2.06 Å20 Å2
3----4.12 Å2
Refinement stepCycle: LAST / Resolution: 1.9→65.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1449 0 34 92 1575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021512
X-RAY DIFFRACTIONr_bond_other_d0.0010.021071
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9672031
X-RAY DIFFRACTIONr_angle_other_deg0.81332578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.95171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.223.33378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51815279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.831513
X-RAY DIFFRACTIONr_chiral_restr0.0620.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021644
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02340
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.899→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 77 -
Rwork0.297 1092 -
obs--98.15 %

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