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- PDB-2i1k: Moesin from Spodoptera frugiperda reveals the coiled-coil domain ... -

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Basic information

Entry
Database: PDB / ID: 2i1k
TitleMoesin from Spodoptera frugiperda reveals the coiled-coil domain at 3.0 angstrom resolution
ComponentsMoesin
KeywordsCell Adhesion / Membrane Protein / FERM / coiled-coil / C-ERMAD / ERM / moesin / radixin / ezrin / merlin / actin binding / masking / regulation / self-inhibition
Function / homology
Function and homology information


adherens junction / animal organ morphogenesis / neuron differentiation / actin binding / cytoskeleton / plasma membrane / cytoplasm
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #10 / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin, alpha-helical domain / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin family C terminal / Acyl-CoA Binding Protein - #10 ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #10 / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin, alpha-helical domain / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin family C terminal / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like / Acyl-CoA Binding Protein / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Helix non-globular / Special / Ubiquitin-like (UB roll) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
UREA / Moesin/ezrin/radixin homolog 1
Similarity search - Component
Biological speciesSpodoptera frugiperda (fall armyworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Refinement against 2.1 angstrom structure / Resolution: 3 Å
AuthorsNance, M.R. / Tesmer, J.J.G.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Self-masking in an Intact ERM-merlin Protein: An Active Role for the Central alpha-Helical Domain.
Authors: Li, Q. / Nance, M.R. / Kulikauskas, R. / Nyberg, K. / Fehon, R. / Karplus, P.A. / Bretscher, A. / Tesmer, J.J.
History
DepositionAug 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Moesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9405
Polymers67,6611
Non-polymers2804
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.940, 126.940, 272.517
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-602-

HOH

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Components

#1: Protein Moesin /


Mass: 67660.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spodoptera frugiperda (fall armyworm) / References: UniProt: A0T1L9
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-URE / UREA / Urea


Mass: 60.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.12 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM HEPES pH 8.0, 15% PEG 8000, 50 mM phosphoserine, 800 mM NaCl, 1 M urea. Crystals were soaked in harvesting solution containing 1 mM IP3 for 2 hours prior to data collection, VAPOR ...Details: 100 mM HEPES pH 8.0, 15% PEG 8000, 50 mM phosphoserine, 800 mM NaCl, 1 M urea. Crystals were soaked in harvesting solution containing 1 mM IP3 for 2 hours prior to data collection, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 112 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationMonochromator: Si(111) double-crystal system / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 17202 / % possible obs: 99.3 % / Rmerge(I) obs: 0.144 / Χ2: 1.022 / Net I/σ(I): 5.6
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3-3.110.43717020.914199.7
3.11-3.230.35216970.919199.7
3.23-3.380.27617040.9821100
3.38-3.560.21217051.074199.6
3.56-3.780.16217181.072199.5
3.78-4.070.12716911.02199
4.07-4.480.10317151.073199.3
4.48-5.130.09817141.061198.8
5.13-6.460.12417481.079199
6.46-500.05118081.009198.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: Refinement against 2.1 angstrom structure
Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.916 / SU B: 9.079 / SU ML: 0.174 / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.249 --
Rwork0.181 --
all0.184 17202 -
obs0.184 17202 99.33 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.964 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.174 Å
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4513 0 17 41 4571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224593
X-RAY DIFFRACTIONr_bond_other_d0.0010.023306
X-RAY DIFFRACTIONr_angle_refined_deg0.9291.9626159
X-RAY DIFFRACTIONr_angle_other_deg0.73737998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9215541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65624.385260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98615910
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5471549
X-RAY DIFFRACTIONr_chiral_restr0.0520.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025071
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02923
X-RAY DIFFRACTIONr_nbd_refined0.1990.2945
X-RAY DIFFRACTIONr_nbd_other0.1690.23243
X-RAY DIFFRACTIONr_nbtor_refined0.170.22177
X-RAY DIFFRACTIONr_nbtor_other0.080.22550
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0980.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1740.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0110.21
X-RAY DIFFRACTIONr_mcbond_it4.22423621
X-RAY DIFFRACTIONr_mcbond_other0.63521092
X-RAY DIFFRACTIONr_mcangle_it5.63944375
X-RAY DIFFRACTIONr_scbond_it10.85962167
X-RAY DIFFRACTIONr_scangle_it13.3781784
LS refinement shellResolution: 3→3.075 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.247 1258 -
obs--99.6 %

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