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

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Basic information

Entry
Database: PDB / ID: 4avg
TitleInfluenza strain pH1N1 2009 polymerase subunit PA endonuclease in complex with diketo compound 2
ComponentsPOLYMERASE PA
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / HYDROLASE / MANGANESE-DEPENDENT
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / 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-SL6 / Polymerase acidic protein
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionMay 25, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_database_status.status_code_sf
Revision 1.2Dec 20, 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 / 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_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

Downloads & links

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Assembly

Deposited unit
A: POLYMERASE PA
B: POLYMERASE PA
C: POLYMERASE PA
D: POLYMERASE PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,87616
Polymers95,7574
Non-polymers2,11912
Water3,261181
1
A: POLYMERASE PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4694
Polymers23,9391
Non-polymers5303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: POLYMERASE PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4694
Polymers23,9391
Non-polymers5303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: POLYMERASE PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4694
Polymers23,9391
Non-polymers5303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: POLYMERASE PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4694
Polymers23,9391
Non-polymers5303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.590, 120.810, 128.200
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 PA / POLYMERASE PA SUBUNIT


Mass: 23939.291 Da / Num. of mol.: 4 / 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-SL6 / (Z)-4-[4-[(4-chlorophenyl)methyl]-1-(cyclohexylmethyl)piperidin-4-yl]-2-oxidanyl-4-oxidanylidene-but-2-enoic acid


Mass: 419.942 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H30ClNO4
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGENBANK NUMBER ACP44156

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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: 2.29 Å3/Da / Density % sol: 46.4 % / Description: NONE
Crystal growpH: 5.5
Details: 25% PEG 3350, 0.1 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS, PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 45289 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.51 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.7
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.44 / % possible all: 99.8

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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: 2.2→43.96 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.434 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25227 2306 5.1 %RANDOM
Rwork0.19578 ---
obs0.19868 42983 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.692 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20 Å2
2---13.5 Å20 Å2
3---12.61 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6480 0 124 181 6785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.026732
X-RAY DIFFRACTIONr_bond_other_d0.0010.024810
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.9639036
X-RAY DIFFRACTIONr_angle_other_deg1.001311605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5395770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2423.352349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.061151254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4051560
X-RAY DIFFRACTIONr_chiral_restr0.1080.2960
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027311
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021485
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: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 158 -
Rwork0.258 3079 -
obs--97.97 %

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