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- PDB-5oo7: The ENTH domain from epsin-2 in complex with phosphatidylinositol... -

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Basic information

Entry
Database: PDB / ID: 5oo7
TitleThe ENTH domain from epsin-2 in complex with phosphatidylinositol 4,5-bisphosphate (PIP2)
ComponentsSLA2
KeywordsENDOCYTOSIS / Phospholipid binding / adaptor protein complex
Function / homology
Function and homology information


clathrin binding / phospholipid binding / endocytosis / actin binding / cytoplasm
Similarity search - Function
Sla2 family / AP180 N-terminal homology (ANTH) domain / ANTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. ...Sla2 family / AP180 N-terminal homology (ANTH) domain / ANTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / ENTH/VHS
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsGarcia-Alai, M. / Meijers, R.
CitationJournal: Nat Commun / Year: 2018
Title: Epsin and Sla2 form assemblies through phospholipid interfaces.
Authors: Garcia-Alai, M.M. / Heidemann, J. / Skruzny, M. / Gieras, A. / Mertens, H.D.T. / Svergun, D.I. / Kaksonen, M. / Uetrecht, C. / Meijers, R.
History
DepositionAug 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rpim_I_all ..._reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rpim_I_all / _reflns_shell.Rmerge_I_obs / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_redundancy
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: SLA2
B: SLA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4443
Polymers59,3522
Non-polymers921
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SLA2
hetero molecules

A: SLA2


Theoretical massNumber of molelcules
Total (without water)59,4443
Polymers59,3522
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y+1/2,-z+11
MethodPISA
Unit cell
Length a, b, c (Å)47.513, 106.280, 51.291
Angle α, β, γ (deg.)90.00, 98.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SLA2


Mass: 29676.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0011900 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0S106
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M potassium bromide, 0.1 M Tris pH 7.5, 8% (w/v) PEG 20K, 8% (w/v) PEG 550 MME.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.84→47 Å / Num. obs: 44311 / % possible obs: 99.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.062 / Net I/σ(I): 8.9
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.42 / Mean I/σ(I) obs: 1 / CC1/2: 0.35 / Rpim(I) all: 0.752

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZYM

3zym


Resolution: 1.84→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.211 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.158 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25181 2178 5 %RANDOM
Rwork0.20373 ---
obs0.20615 41152 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.589 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.01 Å2
2---0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.84→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4176 0 6 395 4577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194328
X-RAY DIFFRACTIONr_bond_other_d0.0010.024016
X-RAY DIFFRACTIONr_angle_refined_deg0.9861.9535856
X-RAY DIFFRACTIONr_angle_other_deg0.84839322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1335521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86723.3203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91715773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.881528
X-RAY DIFFRACTIONr_chiral_restr0.0530.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214773
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02915
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8583.292075
X-RAY DIFFRACTIONr_mcbond_other0.8583.292074
X-RAY DIFFRACTIONr_mcangle_it1.6094.9362599
X-RAY DIFFRACTIONr_mcangle_other1.6094.9372600
X-RAY DIFFRACTIONr_scbond_it0.4923.2992253
X-RAY DIFFRACTIONr_scbond_other0.4923.2992253
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9494.9153258
X-RAY DIFFRACTIONr_long_range_B_refined3.94938.755232
X-RAY DIFFRACTIONr_long_range_B_other3.70438.2445123
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 147 -
Rwork0.305 3051 -
obs--99.29 %

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