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- PDB-2i1j: Moesin from Spodoptera frugiperda at 2.1 angstroms resolution -

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Basic information

Entry
Database: PDB / ID: 2i1j
TitleMoesin from Spodoptera frugiperda at 2.1 angstroms 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


rhabdomere / regulation of organelle assembly / positive regulation of early endosome to late endosome transport / positive regulation of protein localization to early endosome / microvillus / cell adhesion molecule binding / filopodium / animal organ morphogenesis / adherens junction / neuron differentiation ...rhabdomere / regulation of organelle assembly / positive regulation of early endosome to late endosome transport / positive regulation of protein localization to early endosome / microvillus / cell adhesion molecule binding / filopodium / animal organ morphogenesis / adherens junction / neuron differentiation / apical part of cell / regulation of cell shape / actin binding / cytoskeleton / plasma membrane
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #10 / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin family C terminal / Ezrin/radixin/moesin, alpha-helical domain / Acyl-CoA Binding Protein - #10 ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #10 / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin family C terminal / Ezrin/radixin/moesin, alpha-helical domain / 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) / PH-domain like / FERM central domain / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLi, Q. / Nance, 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: Derived calculations / Version format compliance
Revision 1.3Feb 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
Remark 999SEQUENCE AT THE TIME OF PROCESSING, A UNP REFERENCE SEQUENCE WAS NOT AVAILABLE FOR THIS PROTEIN.

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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)68,0937
Polymers67,6611
Non-polymers4326
Water7,404411
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Moesin
hetero molecules

A: Moesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,18514
Polymers135,3212
Non-polymers86412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4220 Å2
ΔGint-35 kcal/mol
Surface area48820 Å2
MethodPISA
3
A: Moesin
hetero molecules

A: Moesin
hetero molecules

A: Moesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,27821
Polymers202,9823
Non-polymers1,29618
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
MethodPQS
Unit cell
Length a, b, c (Å)123.739, 123.739, 283.183
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-656-

HOH

21A-826-

HOH

31A-851-

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


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


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 3.08 Å3/Da / Density % sol: 60.1 %
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, 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: 2→42.72 Å / Num. obs: 43611

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.948 / SU B: 2.248 / SU ML: 0.063 / ESU R: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.215 --
Rwork0.179 --
obs0.176 43611 88.54 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.14 Å20 Å2
2---0.28 Å20 Å2
3---0.42 Å2
Refine analyzeLuzzati coordinate error obs: 0.063 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3972 0 27 411 4410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224094
X-RAY DIFFRACTIONr_bond_other_d0.0010.022941
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.965491
X-RAY DIFFRACTIONr_angle_other_deg1.3137121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2845480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17824.185227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68315803
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0891542
X-RAY DIFFRACTIONr_chiral_restr0.0660.2577
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024513
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02842
X-RAY DIFFRACTIONr_nbd_refined0.1930.2766
X-RAY DIFFRACTIONr_nbd_other0.1830.23044
X-RAY DIFFRACTIONr_nbtor_refined0.170.21925
X-RAY DIFFRACTIONr_nbtor_other0.0850.22215
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2323
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1080.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.22723191
X-RAY DIFFRACTIONr_mcbond_other0.962966
X-RAY DIFFRACTIONr_mcangle_it5.87843883
X-RAY DIFFRACTIONr_scbond_it9.57961945
X-RAY DIFFRACTIONr_scangle_it11.62481608
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.163 2506 -
Rfree-0 -
obs--69.67 %

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