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- PDB-3pr6: Crystal structure analysis of yeast TRAPP associate protein Tca17 -

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Basic information

Entry
Database: PDB / ID: 3pr6
TitleCrystal structure analysis of yeast TRAPP associate protein Tca17
ComponentsTRAPP-associated protein TCA17
KeywordsTRANSPORT PROTEIN / longin fold / vesicle tethering regulation / TRAPP complex / trans-Golgi network
Function / homology
Function and homology information


TRAPPII protein complex / TRAPP complex / early endosome to Golgi transport / intra-Golgi vesicle-mediated transport / retrograde transport, endosome to Golgi / endoplasmic reticulum to Golgi vesicle-mediated transport / protein-containing complex assembly / Golgi apparatus / nucleus / cytosol / cytoplasm
Similarity search - Function
Beta-Lactamase - #70 / Trafficking protein particle complex subunit 2 / Sedlin, N-terminal conserved region / Longin-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TRAPP-associated protein TCA17
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsWang, C. / Gohlke, U. / Heinemann, U.
CitationJournal: Febs J. / Year: 2014
Title: Crystal structure of the yeast TRAPP-associated protein Tca17.
Authors: Wang, C. / Gohlke, U. / Roske, Y. / Heinemann, U.
History
DepositionNov 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRAPP-associated protein TCA17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4803
Polymers18,3531
Non-polymers1282
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TRAPP-associated protein TCA17
hetero molecules

A: TRAPP-associated protein TCA17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9606
Polymers36,7052
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1480 Å2
ΔGint-32 kcal/mol
Surface area16440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.130, 58.492, 53.969
Angle α, β, γ (deg.)90.000, 92.620, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRAPP-associated protein TCA17 / 17 kDa TRAPP complex-associated protein


Mass: 18352.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SYGP-ORF36, TCA17, YEL048C / Plasmid: pGex6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-T1R / References: UniProt: P32613
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG3350, 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 / Wavelength: 0.9796,0.9798,0.9720
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 12, 2010
RadiationMonochromator: Si-111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.97961
30.97981
40.9721
ReflectionResolution: 1.8→29.25 Å / Num. obs: 16453 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 35.308 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 17.49
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.850.40833902121699.5
1.85-1.90.373.43733115499.7
1.9-1.950.2744.53787117699.5
1.95-2.010.1856.336181116100
2.01-2.080.1358.53528109199.4
2.08-2.150.102113512107799.7
2.15-2.230.07913309795899.8
2.23-2.320.06615.93193982100
2.32-2.430.05717.9310995399.7
2.43-2.550.05219.3292390099.9
2.55-2.680.04222.5271483799.6
2.68-2.850.03925.7261181099.3
2.85-3.040.03428.6245775099.2
3.04-3.290.0331.7226870599.4
3.29-3.60.02834.2206465299.1
3.6-4.020.02737.41923597100
4.02-4.650.02738.3164351498.8
4.65-5.690.02438.3140844698.5
5.69-8.050.0337.4104333996.6
8.050.03937.852018090.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
DMphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345data collection
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.2274 / WRfactor Rwork: 0.1874 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8785 / SU B: 5.206 / SU ML: 0.069 / SU R Cruickshank DPI: 0.0257 / SU Rfree: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2196 823 5 %RANDOM
Rwork0.1832 ---
obs0.1851 15631 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 73.75 Å2 / Biso mean: 31.76 Å2 / Biso min: 11.17 Å2
Baniso -1Baniso -2Baniso -3
1--4.04 Å20 Å20.89 Å2
2--0.41 Å20 Å2
3---3.63 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1164 0 7 133 1304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221222
X-RAY DIFFRACTIONr_bond_other_d0.0010.02840
X-RAY DIFFRACTIONr_angle_refined_deg1.2772.0011657
X-RAY DIFFRACTIONr_angle_other_deg0.84932080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2755154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89225.57752
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26915235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.867154
X-RAY DIFFRACTIONr_chiral_restr0.0740.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021318
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02229
X-RAY DIFFRACTIONr_mcbond_it0.7311.5744
X-RAY DIFFRACTIONr_mcbond_other0.1981.5296
X-RAY DIFFRACTIONr_mcangle_it1.3521220
X-RAY DIFFRACTIONr_scbond_it2.1863478
X-RAY DIFFRACTIONr_scangle_it3.7374.5432
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 59 -
Rwork0.203 1127 -
all-1186 -
obs--97.77 %
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)
12.4061-0.19070.01291.5299-0.44140.68020.05930.3195-0.0344-0.2345-0.04930.13620.0714-0.1291-0.010.08760.0275-0.01980.1113-0.02480.154912.6391-5.489316.9869
22.6289-0.7281-0.3630.66450.12490.5730.03950.250.055-0.0497-0.0715-0.02850.03230.06340.0320.10610.00880.00120.1020.01640.148313.26652.979617.4436
34.80944.7151-7.93375.1657-4.073316.5513-0.04960.33980.3387-0.50640.09240.0674-0.2819-0.0038-0.04280.07890.09550.03180.2280.21440.1138.4899.29683.8493
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 59
2X-RAY DIFFRACTION2A60 - 136
3X-RAY DIFFRACTION3A137 - 154

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