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- PDB-4rwb: Racemic influenza M2-TM crystallized from monoolein lipidic cubic... -

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Basic information

Entry
Database: PDB / ID: 4rwb
TitleRacemic influenza M2-TM crystallized from monoolein lipidic cubic phase
ComponentsMatrix protein 2
KeywordsMEMBRANE PROTEIN / transmembrane peptide / proton channel / membrane
Function / homology
Function and homology information


suppression by virus of host autophagy / proton transmembrane transporter activity / : / protein complex oligomerization / monoatomic ion channel activity / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Influenza virus matrix protein 2 / Influenza Matrix protein (M2)
Similarity search - Domain/homology
Chem-MPG / Matrix protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMortenson, D.E. / Steinkruger, J.D. / Kreitler, D.F. / Gellman, S.H. / Forest, K.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: High-resolution structures of a heterochiral coiled coil.
Authors: Mortenson, D.E. / Steinkruger, J.D. / Kreitler, D.F. / Perroni, D.V. / Sorenson, G.P. / Huang, L. / Mittal, R. / Yun, H.G. / Travis, B.R. / Mahanthappa, M.K. / Forest, K.T. / Gellman, S.H.
History
DepositionDec 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Jun 1, 2016Group: Non-polymer description
Revision 1.3Sep 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix protein 2
B: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0285
Polymers4,9582
Non-polymers1,0703
Water724
1
A: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,1923
Polymers2,4791
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,8362
Polymers2,4791
Non-polymers3571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.930, 41.230, 27.930
Angle α, β, γ (deg.)90.000, 95.680, 90.000
Int Tables number14
Space group name H-MP121/c1

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Components

#1: Protein/peptide Matrix protein 2 / Proton channel protein M2


Mass: 2479.123 Da / Num. of mol.: 2 / Fragment: transmembrane domain / Mutation: G34A / Source method: obtained synthetically / Details: Generated via solid-phase peptide synthesis. / Source: (synth.) Influenza A virus / References: UniProt: O70632
#2: Chemical ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.36 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 298 K / Method: monoolein lipidic cubic phase / pH: 6.5
Details: Peptide combined with monoolein at 15-20% (w/w) by codissolving in trifluoroethanol, LCP generated by mixing vacuum-dried solid components with water at 60:40 lipid:water ratio. 200 nL LCP ...Details: Peptide combined with monoolein at 15-20% (w/w) by codissolving in trifluoroethanol, LCP generated by mixing vacuum-dried solid components with water at 60:40 lipid:water ratio. 200 nL LCP bolus combined with 1 uL solution containing 0.1 M ADA pH 6.5, 24% MPD in glass sandwich plates. Crystals grew in less than 1 day. , monoolein lipidic cubic phase, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 14, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→19.39 Å / Num. obs: 6119 / % possible obs: 96.2 % / Redundancy: 7.14 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.127 / Net I/σ(I): 8.88
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsRsym valueDiffraction-ID% possible all
2-2.037.22.271640.56195.9
2.03-2.077.182.593450.491196.4
2.07-2.126.993.343580.421195
2.12-2.177.014.353730.328193
2.17-2.237.233.993500.37196.7
2.23-2.297.155.523590.271196.8
2.29-2.367.044.983550.315193.2
2.36-2.447.325.763430.253197.4
2.44-2.527.186.413230.222196.4
2.52-2.627.197.773360.185196.3
2.62-2.737.268.173230.184196.4
2.73-2.867.159.353090.154195.7
2.86-3.017.3110.463080.128198.7
3.01-3.27.1710.43130.142196
3.2-3.457.2313.113120.103196.9
3.45-3.817.2416.293170.087198.1
3.81-4.377.1317.493120.072197.8
4.37-5.527.0120.363080.064197.5
5.52-19.396.7317.643110.065194.8

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Processing

Software
NameVersionClassificationNB
XPREP2008/2 for Windowsdata reduction
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
EMBLMD-2 softwaredata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LBW

3lbw


Resolution: 2→19.39 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.934 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2956 283 4.8 %RANDOM
Rwork0.2808 ---
obs0.2816 5919 96.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.64 Å2 / Biso mean: 28.352 Å2 / Biso min: 12.77 Å2
Baniso -1Baniso -2Baniso -3
1-2.77 Å2-0 Å2-0.32 Å2
2---2.71 Å20 Å2
3----0.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.194 Å
Refinement stepCycle: LAST / Resolution: 2→19.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms354 0 75 4 433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.019438
X-RAY DIFFRACTIONr_bond_other_d0.0010.02530
X-RAY DIFFRACTIONr_angle_refined_deg1.6412.121579
X-RAY DIFFRACTIONr_angle_other_deg0.79931223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.616544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.808208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.4651564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.944152
X-RAY DIFFRACTIONr_chiral_restr0.0860.275
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.019395
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0277
LS refinement shellResolution: 2→2.108 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.306 41 -
Rwork0.333 800 -
all-841 -
obs-841 96 %

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