- PDB-3etv: Crystal structure of a Tip20p-Dsl1p fusion protein -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3etv
Title
Crystal structure of a Tip20p-Dsl1p fusion protein
Components
Protein transport protein TIP20, Protein transport protein DSL1 chimera
Keywords
TRANSPORT PROTEIN / Tip20p-Dsl1p complex / Endoplasmic reticulum / ER-Golgi transport / Membrane / Phosphoprotein / Protein transport / Transport
Function / homology
Function and homology information
ER-dependent peroxisome organization / RZZ complex / Dsl1/NZR complex / COPI-dependent Golgi-to-ER retrograde traffic / regulation of ER to Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / mitotic spindle assembly checkpoint signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / autophagy / protein transport ...ER-dependent peroxisome organization / RZZ complex / Dsl1/NZR complex / COPI-dependent Golgi-to-ER retrograde traffic / regulation of ER to Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / mitotic spindle assembly checkpoint signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / autophagy / protein transport / endoplasmic reticulum membrane / endoplasmic reticulum / nucleus / cytosol Similarity search - Function
Helix Hairpins - #3290 / Retrograde transport protein Dsl1, N-terminal domain / RINT-1/Tip20 / Protein transport protein Tip20, domain E / Protein transport protein Tip20, domain A / Protein transport protein Tip20, domain B / Protein transport protein Tip20, domain C / RINT-1/TIP-1 family / RINT1/TIP20 domain profile. / Retrograde transport protein Dsl1 N-terminal domain ...Helix Hairpins - #3290 / Retrograde transport protein Dsl1, N-terminal domain / RINT-1/Tip20 / Protein transport protein Tip20, domain E / Protein transport protein Tip20, domain A / Protein transport protein Tip20, domain B / Protein transport protein Tip20, domain C / RINT-1/TIP-1 family / RINT1/TIP20 domain profile. / Retrograde transport protein Dsl1 N-terminal domain / Retrograde transport protein Dsl1, C-terminal domain / Dsl1, N-terminal domain superfamily / Zw10/DSL1, C-terminal / Retrograde transport protein Dsl1 N terminal / Retrograde transport protein Dsl1 C terminal / EXOC6/PINT-1/Sec15/Tip20, C-terminal, domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Sequence details
N-TERMINAL HELIX OF TIP20P IS FUSED TO DSL1P VIA AN EIGHT-RESIDUE GGGSGGGS LINKER
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion / pH: 5 Details: 5:5:1 ratio of protein, well buffer (0.1 M sodium acetate, pH 5.0, 0.2 M ammonium acetate, 20% (w/v) PEG 4000), and additive (1.0 M lithium chloride) , VAPOR DIFFUSION, temperature 298.0K
Monochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.04 Å / Relative weight: 1
Reflection
Resolution: 1.94→100 Å / Num. obs: 25475 / % possible obs: 90.7 % / Redundancy: 3.1 % / Rsym value: 0.057 / Net I/σ(I): 18
Reflection shell
Resolution: 1.94→2.02 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 2691 / Rsym value: 0.467 / % possible all: 97
Resolution: 1.94→40 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.907 / SU B: 4.97 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.27722
1281
5 %
RANDOM
Rwork
0.22453
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obs
0.22737
24166
90.35 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 28.559 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.73 Å2
0 Å2
0.11 Å2
2-
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-1.35 Å2
0 Å2
3-
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0.63 Å2
Refinement step
Cycle: LAST / Resolution: 1.94→40 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2566
0
0
221
2787
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.022
2605
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.091
1.958
3512
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.44
5
312
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.886
25.68
125
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.308
15
508
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.888
15
10
X-RAY DIFFRACTION
r_chiral_restr
0.076
0.2
409
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
1895
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.183
0.2
1219
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.295
0.2
1835
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.131
0.2
192
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.16
0.2
30
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.175
0.2
20
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
2.417
2.5
1639
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
3.328
3.5
2550
X-RAY DIFFRACTION
r_scbond_it
2.63
2.5
1115
X-RAY DIFFRACTION
r_scangle_it
3.516
3.5
962
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.942→1.993 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.349
104
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Rwork
0.293
1806
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obs
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92.49 %
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