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

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Basic information

Entry
Database: PDB / ID: 4awf
TitleInfluenza strain pH1N1 2009 polymerase subunit PA endonuclease in complex with 2 4-dioxo-4-phenylbutanoic acid DPBA
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 / 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
: / 2-4-DIOXO-4-PHENYLBUTANOIC ACID / Polymerase acidic protein
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 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_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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)96,96516
Polymers95,7574
Non-polymers1,20812
Water4,468248
1
A: POLYMERASE PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2414
Polymers23,9391
Non-polymers3023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: POLYMERASE PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2414
Polymers23,9391
Non-polymers3023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: POLYMERASE PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2414
Polymers23,9391
Non-polymers3023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: POLYMERASE PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2414
Polymers23,9391
Non-polymers3023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)260.870, 65.750, 66.030
Angle α, β, γ (deg.)90.00, 95.76, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2028-

HOH

21D-2029-

HOH

31D-2047-

HOH

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Components

#1: Protein
POLYMERASE PA


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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-XI7 / 2-4-DIOXO-4-PHENYLBUTANOIC ACID


Mass: 192.168 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H8O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details2,4-DIOXO-4-PHENYLBUTANOIC ACID (XI7): DPBA

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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: 2.95 Å3/Da / Density % sol: 58.3 % / Description: NONE
Crystal growpH: 7 / Details: 1 M LICL2, 0.1 M HEPES PH 7, 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9474
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9474 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 48474 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 2.43 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.45
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.18 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.18 / % possible all: 95.2

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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: 2.3→46.32 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.856 / SU B: 6.95 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28888 1899 3.9 %RANDOM
Rwork0.2241 ---
obs0.2266 46575 97.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.569 Å2
Baniso -1Baniso -2Baniso -3
1--2.46 Å20 Å2-2.02 Å2
2---0.56 Å20 Å2
3---3.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6240 0 64 248 6552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026417
X-RAY DIFFRACTIONr_bond_other_d0.0010.024527
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.9518600
X-RAY DIFFRACTIONr_angle_other_deg0.928310911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8495735
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90623.211327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.485151199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.21555
X-RAY DIFFRACTIONr_chiral_restr0.0870.2923
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026968
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021431
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: 2.299→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 120 -
Rwork0.297 3289 -
obs--92.36 %

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