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- PDB-4m4q: 6-(4-fluorophenyl)-3-hydroxy-5-[4-(1H-1,2,3,4-tetrazol-5-yl)pheny... -

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Basic information

Entry
Database: PDB / ID: 4m4q
Title6-(4-fluorophenyl)-3-hydroxy-5-[4-(1H-1,2,3,4-tetrazol-5-yl)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 / homologyChem-21A / : / :
Function and homology information
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 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 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Sep 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_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.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)29,0856
Polymers28,5051
Non-polymers5805
Water1629
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)58,17012
Polymers57,0112
Non-polymers1,15910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2400 Å2
ΔGint-70 kcal/mol
Surface area20450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.492, 100.828, 66.616
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 / Mutation: D84A
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, 14 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / 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-21A / 6-(4-fluorophenyl)-5-[4-(1H-tetrazol-5-yl)phenyl]pyridine-2,3-diol


Mass: 349.319 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H12FN5O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3
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 7.3, 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 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2013
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 wavelength
IDWavelength (Å)Relative weight
111
21.11
ReflectionResolution: 2.5→50 Å / Num. obs: 10251 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.106 / Rsym value: 0.116 / Net I/σ(I): 13.09
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3.65 / Rsym value: 0.29 / % possible all: 88.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(PHENIX.REFINE: 1.8.2_1309)model building
PHENIX(phenix.refine: dev_1448)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4KIL

4kil


Resolution: 2.502→29.743 Å / SU ML: 0.27 / σ(F): 14.36 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 512 5 %5%
Rwork0.1963 ---
obs0.1972 10235 97.52 %-
all-10495 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.502→29.743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 34 9 1689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061726
X-RAY DIFFRACTIONf_angle_d1.0132337
X-RAY DIFFRACTIONf_dihedral_angle_d15.523651
X-RAY DIFFRACTIONf_chiral_restr0.044241
X-RAY DIFFRACTIONf_plane_restr0.004296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5017-2.75330.2741180.24332242X-RAY DIFFRACTION92
2.7533-3.15130.27091280.23462443X-RAY DIFFRACTION99
3.1513-3.96880.24061300.20472474X-RAY DIFFRACTION100
3.9688-29.74540.17821360.17732564X-RAY DIFFRACTION99
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)
19.16235.6507-4.22133.7773-2.0035.0242-0.43510.9184-0.5991-0.38910.3561-0.8087-0.18760.83030.09470.8162-0.27880.06320.94840.02980.679121.717617.9522-18.3883
25.52872.27710.56564.9393-0.47515.57940.3335-1.0772-1.2230.6953-0.7117-0.71470.22320.61950.55550.6309-0.164-0.14280.66070.20310.650515.21969.54590.141
36.74331.36422.61557.70362.58288.53350.1475-0.65320.61730.4455-0.41270.6919-0.3909-0.68260.20860.3945-0.03990.02860.4149-0.04110.41543.774218.4733-3.0313
47.88723.2777-2.88153.3381-0.87927.8620.3065-0.7930.37690.331-0.5336-0.2419-1.67931.15840.19810.9021-0.3491-0.09710.66150.03380.603221.039226.078-1.8415
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 83 )
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 149 )
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 195 )

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