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- PDB-4m5o: 3-HYDROXY-6-PHENYL-1,2-DIHYDROPYRIDIN-2-ONE bound to influenza 20... -

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Basic information

Entry
Database: PDB / ID: 4m5o
Title3-HYDROXY-6-PHENYL-1,2-DIHYDROPYRIDIN-2-ONE bound to influenza 2009 H1N1 endonuclease
ComponentsPolymerase PA
KeywordsRNA BINDING PROTEIN/INHIBITOR / CAP-SNATCHING / RNA BINDING PROTEIN-INHIBITOR complex
Function / homology: / 3-hydroxy-6-phenylpyridin-2(5H)-one / :
Function and homology information
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionAug 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Other
Revision 1.2Dec 11, 2013Group: Database references
Revision 1.3Feb 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)29,3909
Polymers28,5051
Non-polymers8858
Water2,504139
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)58,78018
Polymers57,0112
Non-polymers1,76916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2740 Å2
ΔGint-53 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.834, 101.293, 66.154
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: F0TRT1

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Non-polymers , 5 types, 147 molecules

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


Mass: 54.938 Da / Num. of mol.: 3 / 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-X48 / 3-hydroxy-6-phenylpyridin-2(5H)-one


Mass: 187.195 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H9NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging 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, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917 / Wavelength: 0.917 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 4, 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: 0.917 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 44059 / % possible obs: 96.6 % / Observed criterion σ(I): -1 / Redundancy: 3 % / Rmerge(I) obs: 0.082 / Rsym value: 0.064 / Net I/σ(I): 13.29
Reflection shellResolution: 2.01→2.05 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.69 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.2_1309)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.811 Å / SU ML: 0.25 / σ(F): 1.38 / Phase error: 22.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2184 994 4.97 %
Rwork0.182 --
obs0.1838 38003 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→29.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 54 139 1839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131751
X-RAY DIFFRACTIONf_angle_d1.0272373
X-RAY DIFFRACTIONf_dihedral_angle_d16.787652
X-RAY DIFFRACTIONf_chiral_restr0.048241
X-RAY DIFFRACTIONf_plane_restr0.006298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.05410.33321460.33222689X-RAY DIFFRACTION93
2.0541-2.11450.30181400.29142700X-RAY DIFFRACTION95
2.1145-2.18280.28791470.25242740X-RAY DIFFRACTION96
2.1828-2.26080.25961460.23082757X-RAY DIFFRACTION97
2.2608-2.35130.25621480.21572751X-RAY DIFFRACTION97
2.3513-2.45820.29561450.21022776X-RAY DIFFRACTION97
2.4582-2.58770.21231420.18122794X-RAY DIFFRACTION98
2.5877-2.74980.22931470.18122790X-RAY DIFFRACTION98
2.7498-2.96190.21941440.17572822X-RAY DIFFRACTION99
2.9619-3.25960.21611440.1722821X-RAY DIFFRACTION99
3.2596-3.73050.18771490.16282828X-RAY DIFFRACTION99
3.7305-4.69710.18111450.13972838X-RAY DIFFRACTION100
4.6971-29.81450.1991460.16792808X-RAY DIFFRACTION98
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)
14.62192.1854-0.32913.6645-0.43932.5935-0.26490.1461-0.3098-0.2438-0.0153-0.22330.22470.42370.23020.3095-0.0642-0.02580.27290.00990.282919.192415.7566-10.3552
22.68640.59020.69664.1514-0.87625.01990.2704-0.3631-0.2440.1109-0.3164-0.0310.2549-0.44120.00970.2355-0.0746-0.02660.25550.01840.28747.064411.0327-2.338
35.65742.6112-1.55692.3963-0.88315.3098-0.0207-0.08810.76430.059-0.10250.3956-0.90150.04850.01110.4466-0.0923-0.07220.2349-0.04860.387516.021926.1403-1.9962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 126 )
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 195 )

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