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- PDB-4mk1: 5-bromopyridine-2,3-diol bound to influenza 2009 pH1N1 endonuclease -

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Basic information

Entry
Database: PDB / ID: 4mk1
Title5-bromopyridine-2,3-diol bound to influenza 2009 pH1N1 endonuclease
ComponentsPOLYMERASE PA
KeywordsRNA BINDING PROTEIN/INHIBITOR / CAP-SNATCHING / RNA BINDING PROTEIN / RNA BINDING PROTEIN-INHIBITOR complex
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
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-bromo-3-hydroxypyridin-2(1H)-one / : / Polymerase acidic protein
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBauman, J.D. / Patel, D. / Das, K. / Arnold, E.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Crystallographic fragment screening and structure-based optimization yields a new class of influenza endonuclease inhibitors.
Authors: Bauman, J.D. / Patel, D. / Baker, S.F. / Vijayan, R.S. / Xiang, A. / Parhi, A.K. / Martinez-Sobrido, L. / Lavoie, E.J. / Das, K. / Arnold, E.
History
DepositionSep 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,45310
Polymers28,5051
Non-polymers9489
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: POLYMERASE PA
hetero molecules

A: POLYMERASE PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,90620
Polymers57,0112
Non-polymers1,89618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3180 Å2
ΔGint-72 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.932, 101.655, 66.212
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein POLYMERASE PA


Mass: 28505.270 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS (A/LIMA/WRAIR1695P/2009(H1N1))
Gene: PA / Plasmid: PCDF-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: M9V5A4

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Non-polymers , 5 types, 143 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-27Y / 5-bromo-3-hydroxypyridin-2(1H)-one


Mass: 189.995 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H4BrNO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 200 MM MES, 27% PEG8K, 200 MM AMMONIUM SULFATE, 1 MM MANGANESE CHLORIDE, 10 MM MAGNESIUM ACETATE, 10 MM TAURINE, AND 50 MM SODIUM FLUORIDE, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2012
RadiationMonochromator: HORIZONTAL BENT SI(111), ASYMMETRICALLY CUT WITH WATER COOLED CU BLOCK
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 25915 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 40.565
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 4.45 / % possible all: 96.1

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIX(PHENIX.REFINE: 1.8.2_1309)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→40.318 Å / SU ML: 0.19 / σ(F): 1.36 / Phase error: 19.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1976 1321 5.1 %
Rwork0.1763 --
obs0.1774 25892 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→40.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 40 134 1820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081734
X-RAY DIFFRACTIONf_angle_d1.152349
X-RAY DIFFRACTIONf_dihedral_angle_d14.377640
X-RAY DIFFRACTIONf_chiral_restr0.056241
X-RAY DIFFRACTIONf_plane_restr0.007295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8495-1.92360.26661510.22542607X-RAY DIFFRACTION97
1.9236-2.01110.19911320.19482715X-RAY DIFFRACTION99
2.0111-2.11710.21271490.18162696X-RAY DIFFRACTION100
2.1171-2.24980.19321420.16322714X-RAY DIFFRACTION100
2.2498-2.42350.1861620.17612715X-RAY DIFFRACTION100
2.4235-2.66730.21581460.17222705X-RAY DIFFRACTION100
2.6673-3.05310.20591360.18092769X-RAY DIFFRACTION100
3.0531-3.84620.20791480.17722764X-RAY DIFFRACTION100
3.8462-40.32750.18091550.17192886X-RAY DIFFRACTION100
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)
17.6583.3447-1.3625.5156-2.26215.434-0.35590.63-0.2279-0.32170.2336-0.00120.2150.09230.11370.3782-0.07670.01310.3533-0.02490.213521.63718.6834-18.5191
25.80882.7655-0.56627.9805-4.92948.9247-0.0168-0.5505-0.63970.1764-0.1355-0.18930.4195-0.18980.28920.2643-0.0656-0.01410.23480.03460.276316.506112.7116-0.7684
31.4020.5855-1.27764.0791-3.46993.4240.1357-0.3208-0.99620.2022-0.3357-0.69660.34290.21060.12740.424-0.0833-0.10990.30270.10870.586314.44174.77210.6885
43.59091.06311.17021.96521.47266.56280.339-0.30280.20390.2379-0.39040.49530.2983-0.91410.01420.2201-0.0307-0.02480.2944-0.01490.30733.582214.0849-3.6307
57.8788-0.7528-0.66778.4952-3.31243.24150.15110.11621.2863-0.0317-0.05971.075-0.6482-0.7087-0.12740.48260.0427-0.02330.3899-0.08250.55545.209326.5018-1.2992
64.91251.9061-1.57861.8397-0.7655.3784-0.048-0.17190.5187-0.0391-0.07440.103-0.64750.57310.01850.3998-0.1425-0.06830.2542-0.02410.328621.35726.0343-1.8664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 62 )
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 83 )
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 126 )
5X-RAY DIFFRACTION5chain 'A' and (resid 127 through 149 )
6X-RAY DIFFRACTION6chain 'A' and (resid 150 through 195 )

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