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- PDB-1sz7: Crystal structure of Human Bet3 -

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Basic information

Entry
Database: PDB / ID: 1sz7
TitleCrystal structure of Human Bet3
ComponentsTrafficking protein particle complex subunit 3
KeywordsTRANSPORT PROTEIN / ALPHA-BETA PLAIT / TRAPP COMPLEX / PALMITOYLATED
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 membrane / COPII-mediated vesicle transport ...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 membrane / COPII-mediated vesicle transport / endoplasmic reticulum to Golgi vesicle-mediated transport / Golgi membrane / Golgi apparatus / endoplasmic reticulum / cytosol / cytoplasm
Similarity search - Function
Trafficking protein particle complex subunit 3 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsTurnbull, A.P. / Prinz, B. / Holz, C. / Behlke, J. / Schultchen, J. / Delbrueck, H. / Niesen, F.H. / Lang, C. / Heinemann, U.
CitationJournal: Embo J. / Year: 2005
Title: Structure of palmitoylated BET3: insights into TRAPP complex assembly and membrane localization
Authors: Turnbull, A.P. / Prinz, B. / Holz, C. / Schultchen, J. / Lang, C.
History
DepositionApr 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trafficking protein particle complex subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8682
Polymers22,6121
Non-polymers2561
Water2,216123
1
A: Trafficking protein particle complex subunit 3
hetero molecules

A: Trafficking protein particle complex subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7364
Polymers45,2232
Non-polymers5132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4550 Å2
ΔGint-27 kcal/mol
Surface area13870 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.901, 72.901, 56.803
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a dimer generated by the two-fold axis: y,x,-z

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Components

#1: Protein Trafficking protein particle complex subunit 3 / BET3 homolog


Mass: 22611.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAPPC3, BET3 / Plasmid: pYEXTHS-BN / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): AH22ura3 / References: UniProt: O43617
#2: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


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


Mass: 18.015 Da / Num. of mol.: 123 / 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: 1.9 Å3/Da / Density % sol: 35.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG400, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.978573 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 16, 2003 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978573 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. all: 24929 / Num. obs: 24929 / % possible obs: 97 % / Redundancy: 3.5 % / Rsym value: 0.055 / Net I/σ(I): 20.3
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 1126 / Rsym value: 0.48 / % possible all: 89.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.716 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24516 1269 5.1 %RANDOM
Rwork0.20702 ---
obs-23658 97.11 %-
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 mean: 21.231 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 17 123 1370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221266
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.9721704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1315158
X-RAY DIFFRACTIONr_chiral_restr0.090.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02932
X-RAY DIFFRACTIONr_nbd_refined0.2280.2576
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.278
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.214
X-RAY DIFFRACTIONr_mcbond_it0.8791.5785
X-RAY DIFFRACTIONr_mcangle_it1.64521264
X-RAY DIFFRACTIONr_scbond_it2.5833481
X-RAY DIFFRACTIONr_scangle_it4.0894.5440
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.288 71
Rwork0.281 1627

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