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- PDB-5wfb: Tepsin tENTH domain 1-136. -

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Basic information

Entry
Database: PDB / ID: 5wfb
TitleTepsin tENTH domain 1-136.
ComponentsAP-4 complex accessory subunit Tepsin
KeywordsPROTEIN TRANSPORT / protein trafficking
Function / homology
Function and homology information


coated vesicle membrane / extrinsic component of organelle membrane / trans-Golgi network membrane / nuclear membrane / nuclear speck / Golgi apparatus / cytoplasm / cytosol
Similarity search - Function
Tepsin, ENTH/VHS domain / AP-4 complex accessory subunit Tepsin / ENTH domain / ENTH domain / ENTH/VHS
Similarity search - Domain/homology
AP-4 complex accessory subunit Tepsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.382 Å
AuthorsArchuleta, T.L. / Jackson, L.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM119525 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)T32MH65215-12 United States
CitationJournal: Traffic / Year: 2017
Title: Structure and evolution of ENTH and VHS/ENTH-like domains in tepsin.
Authors: Archuleta, T.L. / Frazier, M.N. / Monken, A.E. / Kendall, A.K. / Harp, J. / McCoy, A.J. / Creanza, N. / Jackson, L.P.
History
DepositionJul 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AP-4 complex accessory subunit Tepsin
B: AP-4 complex accessory subunit Tepsin


Theoretical massNumber of molelcules
Total (without water)31,2622
Polymers31,2622
Non-polymers00
Water3,207178
1
A: AP-4 complex accessory subunit Tepsin


Theoretical massNumber of molelcules
Total (without water)15,6311
Polymers15,6311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AP-4 complex accessory subunit Tepsin


Theoretical massNumber of molelcules
Total (without water)15,6311
Polymers15,6311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.870, 84.750, 80.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein AP-4 complex accessory subunit Tepsin / ENTH domain-containing protein 2 / Epsin for AP-4 / Tetra-epsin


Mass: 15631.050 Da / Num. of mol.: 2 / Fragment: UNP residues 1-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEPSIN, C17orf56, ENTHD2 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q96N21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 12% (w/v) PEG3350, 4% (v/v) tacsimate pH 5.0

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.38→19.821 Å / Num. obs: 56820 / % possible obs: 99.6 % / Redundancy: 12.1 % / Rsym value: 1.042 / Net I/σ(I): 14.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: basic alpha helical model

Resolution: 1.382→19.821 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.17
RfactorNum. reflection% reflection
Rfree0.1853 2879 5.07 %
Rwork0.1562 --
obs0.1577 56820 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.382→19.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 0 178 2199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122071
X-RAY DIFFRACTIONf_angle_d1.0512803
X-RAY DIFFRACTIONf_dihedral_angle_d12.029763
X-RAY DIFFRACTIONf_chiral_restr0.072315
X-RAY DIFFRACTIONf_plane_restr0.01359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.382-1.40460.27191440.23992535X-RAY DIFFRACTION100
1.4046-1.42880.27991200.22372574X-RAY DIFFRACTION100
1.4288-1.45480.23551390.20462491X-RAY DIFFRACTION100
1.4548-1.48280.221340.18852557X-RAY DIFFRACTION100
1.4828-1.51310.20471400.17142534X-RAY DIFFRACTION99
1.5131-1.54590.20681460.16952474X-RAY DIFFRACTION98
1.5459-1.58190.19271460.15632560X-RAY DIFFRACTION100
1.5819-1.62140.22161210.15172546X-RAY DIFFRACTION100
1.6214-1.66520.18061420.13852545X-RAY DIFFRACTION100
1.6652-1.71420.16741490.13142558X-RAY DIFFRACTION100
1.7142-1.76950.19941260.13722575X-RAY DIFFRACTION100
1.7695-1.83270.17491270.13542579X-RAY DIFFRACTION100
1.8327-1.9060.19011370.14512559X-RAY DIFFRACTION100
1.906-1.99270.19231350.14842566X-RAY DIFFRACTION100
1.9927-2.09770.18971230.14292586X-RAY DIFFRACTION100
2.0977-2.22890.16881320.1412560X-RAY DIFFRACTION99
2.2289-2.40080.16441740.14172554X-RAY DIFFRACTION100
2.4008-2.64180.15681290.14082609X-RAY DIFFRACTION100
2.6418-3.0230.16561370.16342610X-RAY DIFFRACTION100
3.023-3.80420.19891470.16542622X-RAY DIFFRACTION100
3.8042-19.8230.18691310.16452749X-RAY DIFFRACTION100

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