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- PDB-2c0j: Crystal structure of the bet3-trs33 heterodimer -

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Basic information

Entry
Database: PDB / ID: 2c0j
TitleCrystal structure of the bet3-trs33 heterodimer
Components
  • R32611_2
  • TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3
KeywordsTRANSPORT / TRANSPORT PROTEIN / ENDOPLASMIC RETICULUM / ER-GOLGI TRANSPORT / LIPOPROTEIN / PALMITATE
Function / homology
Function and homology information


vesicle coating / vesicle tethering / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / COPII vesicle coating / intra-Golgi vesicle-mediated transport / RAB GEFs exchange GTP for GDP on RABs / cis-Golgi network / cis-Golgi network membrane ...vesicle coating / vesicle tethering / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / COPII vesicle coating / intra-Golgi vesicle-mediated transport / RAB GEFs exchange GTP for GDP on RABs / cis-Golgi network / cis-Golgi network membrane / COPII-mediated vesicle transport / endoplasmic reticulum to Golgi vesicle-mediated transport / trans-Golgi network / Golgi membrane / Golgi apparatus / endoplasmic reticulum / cytosol / cytoplasm
Similarity search - Function
Trafficking protein particle complex subunit 3 / TRAPP complex, Trs33 subunit / Bet3 family / Transport protein particle (TRAPP) component / Transport protein particle (TRAPP) component / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / NO signalling/Golgi transport ligand-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / Trafficking protein particle complex subunit 3 / Trafficking protein particle complex subunit 6A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.2 Å
AuthorsKim, M.-S. / Yi, M.-J. / Lee, K.-H. / Wagner, J. / Munger, C. / Kim, Y.-G. / Whiteway, M. / Cygler, M. / Oh, B.-H. / Sacher, M.
CitationJournal: Traffic / Year: 2005
Title: Biochemical and Crystallographic Studies Reveal a Specific Interaction between Trapp Subunits Trs33P and Bet3P
Authors: Kim, M.-S. / Yi, M.-J. / Lee, K.-H. / Wagner, J. / Munger, C. / Kim, Y.-G. / Whiteway, M. / Cygler, M. / Oh, B.-H. / Sacher, M.
History
DepositionSep 3, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jan 14, 2015Group: Derived calculations

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3
B: R32611_2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1653
Polymers35,9082
Non-polymers2561
Water1,20767
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-19.1 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.877, 70.515, 88.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3 / BET3-TRS33 COMPLEX / BET3 HOMOLOG


Mass: 18230.748 Da / Num. of mol.: 1 / Fragment: RESIDUES 15-175
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O43617
#2: Protein R32611_2


Mass: 17677.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O75865
#3: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 43 %

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 15881 / % possible obs: 92.1 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.2→10 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.2368 789 4.6 %RANDOM
Rwork0.2187 ---
obs0.2187 15881 92.1 %-
Solvent computationBsol: 47.0909 Å2 / ksol: 0.456723 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.632 Å20 Å20 Å2
2---5.084 Å20 Å2
3----4.547 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 17 67 2486
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006677
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.17508
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3PLM.PAR

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