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- PDB-4rwc: Racemic M2-TM crystallized from racemic detergent -

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Basic information

Entry
Database: PDB / ID: 4rwc
TitleRacemic M2-TM crystallized from racemic detergent
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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,3564
Polymers2,4791
Non-polymers8773
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)15.350, 25.880, 26.970
Angle α, β, γ (deg.)90.010, 99.490, 99.910
Int Tables number2
Space group name H-MP-1

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Components

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


Mass: 2479.123 Da / Num. of mol.: 1 / 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: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Racemic M2-TM dissolved at ~3 mg/mL in 2% solution (w/v) racemic OG. Hanging drops of 1 uL peptide stock combined with 1 uL of precipitant containing 0.1 M ADA pH 6.5, 1.0 M ammonium sulfate ...Details: Racemic M2-TM dissolved at ~3 mg/mL in 2% solution (w/v) racemic OG. Hanging drops of 1 uL peptide stock combined with 1 uL of precipitant containing 0.1 M ADA pH 6.5, 1.0 M ammonium sulfate were equilibrated with 500 uL reservoir volumes of precipitant., VAPOR DIFFUSION, HANGING DROP, 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 9, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.05→26.59 Å / Num. obs: 17458 / % possible obs: 92.6 % / Redundancy: 6.01 % / Biso Wilson estimate: 5.3 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 12.89
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsDiffraction-ID% possible all
1.05-1.082.540.3812.54702165.9
1.08-1.113.330.313.331224185.2
1.11-1.143.640.2663.641126191.4
1.14-1.173.530.1843.531024189.2
1.17-1.23.540.1883.54934189.4
1.2-1.246.310.3056.311136194.3
1.24-1.287.150.2857.151006193.4
1.28-1.337.390.2417.391100195.2
1.33-1.387.310.2127.31948194.4
1.38-1.447.40.1947.4983196
1.44-1.517.430.1317.43963195.7
1.51-1.597.420.1197.42894196.5
1.59-1.697.490.097.49908197
1.69-1.837.510.0827.51948197.6
1.83-2.027.440.0647.44904198
2.02-2.317.330.0517.33886198.4
2.31-2.917.280.0447.28895199.1
2.91-26.596.790.0376.79877198.1

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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 / Resolution: 1.05→26.59 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.553 / SU ML: 0.012 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1556 867 5 %RANDOM
Rwork0.1383 ---
obs0.1392 17310 91.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.12 Å2 / Biso mean: 14.015 Å2 / Biso min: 5.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20.49 Å2-0.35 Å2
2--0.67 Å21.36 Å2
3----0.53 Å2
Refine analyzeLuzzati coordinate error obs: 0.021 Å
Refinement stepCycle: LAST / Resolution: 1.05→26.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms177 0 36 28 241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.019244
X-RAY DIFFRACTIONr_bond_other_d0.0010.02307
X-RAY DIFFRACTIONr_angle_refined_deg1.5512.143329
X-RAY DIFFRACTIONr_angle_other_deg0.7513710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.961529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.953204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.271539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1.048151
X-RAY DIFFRACTIONr_chiral_restr0.080.249
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02204
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0239
X-RAY DIFFRACTIONr_rigid_bond_restr2.093551
X-RAY DIFFRACTIONr_sphericity_free29.37354
X-RAY DIFFRACTIONr_sphericity_bonded20.6145572
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 57 -
Rwork0.242 922 -
all-979 -
obs-979 69.38 %

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