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- PDB-5ucc: Crystal structure of the ENTH domain of ENT2 from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 5ucc
TitleCrystal structure of the ENTH domain of ENT2 from Candida albicans
ComponentsPotential epsin-like clathrin-binding protein
KeywordsLIPID BINDING PROTEIN / ENTH domain / predicted lipid binding protein / endocytosis / all alpha protein / structural genomics / center for structural genomics of infectious diseases / CSGID / NIAID / national institute of allergy and infectious diseases
Function / homology
Function and homology information


clathrin vesicle coat / clathrin binding / actin filament organization / phospholipid binding / endocytosis / endosome / intracellular membrane-bounded organelle / plasma membrane
Similarity search - Function
ENTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / Ubiquitin interaction motif / ENTH/VHS / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. ...ENTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / Ubiquitin interaction motif / ENTH/VHS / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / Epsin / :
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsStogios, P.J. / Evdokimova, E. / Di Leo, R. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSCN27220120026C United States
CitationJournal: To Be Published
Title: Crystal structure of the ENTH domain of ENT2 from Candida albicans
Authors: Stogios, P.J.
History
DepositionDec 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.title / _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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: Potential epsin-like clathrin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6357
Polymers18,1091
Non-polymers5266
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.901, 88.901, 67.259
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Potential epsin-like clathrin-binding protein


Mass: 18108.605 Da / Num. of mol.: 1 / Fragment: UNP residues 1-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: ENT2, orf19.1444, CaO19.1444 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: Q5AMD1, UniProt: A0A1D8PGB7*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M sodium chloride, 0.1M phosphate-citrate pH 4.2, 20% (w/v) PEG8K, 0.3 M NDSB195

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.83→25 Å / Num. obs: 17422 / % possible obs: 99.3 % / Redundancy: 6.5 % / Rsym value: 0.066 / Net I/σ(I): 41.76
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.185 / Mean I/σ(I) obs: 2.04 / CC1/2: 0.522 / Rpim(I) all: 0.527 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GZC

4gzc


Resolution: 1.83→22.42 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.92
RfactorNum. reflection% reflectionSelection details
Rfree0.1846 863 4.95 %RANDOM
Rwork0.1565 ---
obs0.158 17420 99.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.83→22.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 30 215 1353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081180
X-RAY DIFFRACTIONf_angle_d0.9471597
X-RAY DIFFRACTIONf_dihedral_angle_d25.161463
X-RAY DIFFRACTIONf_chiral_restr0.06173
X-RAY DIFFRACTIONf_plane_restr0.007209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8265-1.94090.33131430.27372723X-RAY DIFFRACTION97
1.9409-2.09060.22661430.19812707X-RAY DIFFRACTION99
2.0906-2.30080.19281430.15572776X-RAY DIFFRACTION99
2.3008-2.63330.18561430.16042784X-RAY DIFFRACTION100
2.6333-3.3160.20881470.15772778X-RAY DIFFRACTION100
3.316-22.42130.15291440.13782789X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.6345-5.4044-6.48085.17836.13827.8652-0.2425-0.306-0.17350.69880.34820.57330.2698-0.1136-0.2550.35270.00250.01370.3070.06130.295-16.8112-26.498320.3542
26.1904-1.01641.43092.9177-1.57519.49340.05910.1793-0.3676-0.0783-0.0747-0.07970.7004-0.0475-0.02020.2773-0.0310.01690.16210.00920.2449-7.2598-29.941214.8009
37.3474-6.2568-5.96175.32785.07964.842-0.029-0.0251-0.16110.1866-0.01550.5418-0.1842-0.37110.21640.2853-0.04780.01180.33290.010.2962-19.2036-18.263512.8588
42.9818-1.5499-1.05573.9658-0.21882.6979-0.10210.04920.01590.27240.07780.0098-0.0082-0.04420.00980.226-0.0536-0.01430.1854-0.00680.2111-9.4827-16.265612.2252
58.5935-5.034-3.24937.55853.43212.8433-0.3971-0.5324-0.00850.98990.21390.20510.1404-0.0570.1980.42340.0084-0.00480.29690.00610.278-12.1496-6.468517.8901
66.5709-1.63541.41682.15810.76347.50350.3126-0.1483-0.53390.0458-0.0242-0.54340.48990.4442-0.15490.2346-0.0221-0.04330.2690.00710.35857.3785-19.171311.409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 15:32)
2X-RAY DIFFRACTION2(chain A and resid 33:57)
3X-RAY DIFFRACTION3(chain A and resid 58:68)
4X-RAY DIFFRACTION4(chain A and resid 69:112)
5X-RAY DIFFRACTION5(chain A and resid 113:131)
6X-RAY DIFFRACTION6(chain A and resid 132:149)

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