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- PDB-2he7: FERM domain of EPB41L3 (DAL-1) -

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Basic information

Entry
Database: PDB / ID: 2he7
TitleFERM domain of EPB41L3 (DAL-1)
ComponentsBand 4.1-like protein 3
KeywordsCELL ADHESION / FERM domain / DAL-1 / EPB41L3A / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


protein localization to paranode region of axon / cytoskeletal protein-membrane anchor activity / paranodal junction assembly / protein localization to juxtaparanode region of axon / myelin maintenance / paranode region of axon / cortical cytoskeleton organization / actomyosin structure organization / juxtaparanode region of axon / Neurexins and neuroligins ...protein localization to paranode region of axon / cytoskeletal protein-membrane anchor activity / paranodal junction assembly / protein localization to juxtaparanode region of axon / myelin maintenance / paranode region of axon / cortical cytoskeleton organization / actomyosin structure organization / juxtaparanode region of axon / Neurexins and neuroligins / Sensory processing of sound by inner hair cells of the cochlea / Sensory processing of sound by outer hair cells of the cochlea / cortical actin cytoskeleton organization / neuron projection morphogenesis / protein localization to plasma membrane / structural constituent of cytoskeleton / cell-cell junction / cell junction / actin binding / regulation of cell shape / cytoskeleton / apoptotic process / plasma membrane / cytosol
Similarity search - Function
Band 4.1-like protein 3 / SAB domain / Band 4.1, C-terminal / SAB domain / 4.1 protein C-terminal domain (CTD) / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like ...Band 4.1-like protein 3 / SAB domain / Band 4.1, C-terminal / SAB domain / 4.1 protein C-terminal domain (CTD) / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / 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 / 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
Band 4.1-like protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHallberg, B.M. / Busam, R.D. / Arrowsmith, C. / Berglund, H. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. ...Hallberg, B.M. / Busam, R.D. / Arrowsmith, C. / Berglund, H. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Schiavone, L.H. / Johansson, I. / Hogbom, M. / Karlberg, T. / Kotenyova, T. / Nilvebrandt, J. / Norberg, P. / Stenmark, P. / Nordlund, P. / Nilsson-ehle, P. / Nyman, T. / Ogg, D. / Sagemark, J. / Sundstrom, M. / Uppenberg, J. / Van den berg, S. / Weigelt, J. / Persson, C. / Thorsell, A.G. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural basis of tumor suppressor in lung cancer 1 (TSLC1) binding to differentially expressed in adenocarcinoma of the lung (DAL-1/4.1B).
Authors: Busam, R.D. / Thorsell, A.G. / Flores, A. / Hammarstrom, M. / Persson, C. / Obrink, B. / Hallberg, B.M.
History
DepositionJun 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Band 4.1-like protein 3


Theoretical massNumber of molelcules
Total (without water)33,0801
Polymers33,0801
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.500, 135.500, 49.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Band 4.1-like protein 3 / 4.1B / Differentially expressed in adenocarcinoma of the lung protein 1 / DAL-1


Mass: 33079.918 Da / Num. of mol.: 1 / Fragment: FERM domain (Residues 108-390)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPB41L3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2J2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 4 Å3/Da / Density % sol: 69.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% EtOH 0.1 M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 22, 2006 / Details: Double crystal monochromator
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 35521 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 36.146 Å2 / Rsym value: 0.08 / Net I/σ(I): 21.13
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
2-2.10.5614.852182470998.4
2.1-2.20.3976.743700392099.2
2.2-2.30.38.936977331899.4
2.3-2.40.23410.831030277399.4
2.4-2.50.18613.126157234599.7
2.5-2.60.15315.622418200699.6
2.6-2.70.12118.819149171799.7
2.7-30.08923.643680391499.7
3-40.06132.666589611399.8
4-50.04843.223338219999.8
5-60.0364.210285976100
60.02570.1113921079100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.34 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.495 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1779 5 %RANDOM
Rwork0.187 ---
all0.188 35521 --
obs0.188 35521 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.172 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.16 Å20 Å2
2---0.32 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2323 0 0 247 2570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222521
X-RAY DIFFRACTIONr_bond_other_d0.0010.021791
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.9543416
X-RAY DIFFRACTIONr_angle_other_deg0.98234334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2415309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30723.101129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93115459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2611522
X-RAY DIFFRACTIONr_chiral_restr0.1040.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022861
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02561
X-RAY DIFFRACTIONr_nbd_refined0.2110.2466
X-RAY DIFFRACTIONr_nbd_other0.1940.21817
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21199
X-RAY DIFFRACTIONr_nbtor_other0.0910.21350
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2178
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0960.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.221
X-RAY DIFFRACTIONr_mcbond_it1.6781.51930
X-RAY DIFFRACTIONr_mcbond_other0.2861.5597
X-RAY DIFFRACTIONr_mcangle_it1.89422425
X-RAY DIFFRACTIONr_scbond_it3.12631195
X-RAY DIFFRACTIONr_scangle_it4.3254.5991
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 114 -
Rwork0.263 2479 -
obs-2593 99.96 %

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