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- PDB-4m5q: High-resolution apo influenza 2009 H1N1 endonuclease structure -

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Basic information

Entry
Database: PDB / ID: 4m5q
TitleHigh-resolution apo influenza 2009 H1N1 endonuclease structure
ComponentsPolymerase PA
KeywordsRNA BINDING PROTEIN / CAP-SNATCHING
Function / homology: / :
Function and homology information
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.534 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)28,7325
Polymers28,5051
Non-polymers2274
Water4,053225
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)57,46410
Polymers57,0112
Non-polymers4548
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3020 Å2
ΔGint-47 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.400, 101.490, 66.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-578-

HOH

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Components

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


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.6 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: 1.53→50.75 Å / Num. obs: 250493 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 16.2
Reflection shellResolution: 1.53→1.62 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 3.2 / % possible all: 97.7

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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: 1.534→46.9 Å / SU ML: 0.1 / σ(F): 1.34 / Phase error: 20.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1839 889 2 %
Rwork0.1707 --
obs0.1709 44527 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.534→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1657 0 7 225 1889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131728
X-RAY DIFFRACTIONf_angle_d1.3992335
X-RAY DIFFRACTIONf_dihedral_angle_d14.263655
X-RAY DIFFRACTIONf_chiral_restr0.092244
X-RAY DIFFRACTIONf_plane_restr0.008298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.534-1.63010.21781440.20927038X-RAY DIFFRACTION98
1.6301-1.7560.19711480.17887206X-RAY DIFFRACTION100
1.756-1.93270.1941470.16157258X-RAY DIFFRACTION100
1.9327-2.21240.1911480.15657263X-RAY DIFFRACTION100
2.2124-2.78730.15951480.17087330X-RAY DIFFRACTION100
2.7873-46.92220.18671540.17227543X-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)
14.81371.8646-0.17364.0887-1.56124.1791-0.14370.2958-0.1487-0.19430.11610.05060.1995-0.06350.01060.1788-0.03470.01450.1958-0.02870.120921.468418.8248-18.3437
23.14892.1846-1.92282.5645-3.07087.7428-0.08070.1704-0.0663-0.08130.0885-0.0306-0.03550.03380.03110.1843-0.0565-0.01040.141-0.0150.170817.808118.716-8.7687
34.5680.8343-1.24958.5324-4.36298.01160.3376-1.0538-0.99641.2379-0.135-0.15230.4213-0.69360.02520.5109-0.145-0.06180.52590.17790.412214.57914.575710.1107
41.56940.637-0.09673.6382-2.89254.32680.2329-0.1294-0.58440.0671-0.5355-0.72530.49010.72110.16370.3111-0.043-0.07870.27330.10580.400814.54494.60280.8395
52.1546-0.22120.31851.41490.83235.26040.2527-0.26110.01510.1328-0.29140.35670.3429-0.79640.00890.1543-0.0575-0.03590.22590.00520.21093.666313.8237-3.5046
65.236-0.7536-1.68228.7428-2.18918.16380.09180.15270.6503-0.02930.18041.0451-0.5539-0.854-0.19110.24480.0322-0.01220.26610.00410.32635.211326.3026-1.066
72.42490.8441-1.97250.7527-0.37125.40310.0816-0.03390.2654-0.0251-0.0510.0754-0.53810.2263-0.02290.2115-0.0766-0.02950.1655-0.02830.191420.866726.1661-1.8345
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 49 )
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 62 )
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 83 )
5X-RAY DIFFRACTION5chain 'A' and (resid 84 through 126 )
6X-RAY DIFFRACTION6chain 'A' and (resid 127 through 149 )
7X-RAY DIFFRACTION7chain 'A' and (resid 150 through 196 )

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