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- PDB-2c5j: N-terminal domain of tlg1, domain-swapped dimer -

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Basic information

Entry
Database: PDB / ID: 2c5j
TitleN-terminal domain of tlg1, domain-swapped dimer
ComponentsT-SNARE AFFECTING A LATE GOLGI COMPARTMENT PROTEIN 1
KeywordsPROTEIN TRANSPORT / SNARE / TRANSPORT / PHOSPHORYLATION
Function / homology
Function and homology information


Retrograde transport at the Trans-Golgi-Network / Golgi vesicle fusion to target membrane / vesicle fusion with Golgi apparatus / Golgi to endosome transport / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / retrograde transport, endosome to Golgi / endomembrane system ...Retrograde transport at the Trans-Golgi-Network / Golgi vesicle fusion to target membrane / vesicle fusion with Golgi apparatus / Golgi to endosome transport / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / retrograde transport, endosome to Golgi / endomembrane system / SNARE binding / intracellular protein transport / trans-Golgi network / endocytosis / late endosome membrane / early endosome membrane / endosome membrane / endosome / Golgi membrane / cytosol
Similarity search - Function
: / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...: / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
t-SNARE affecting a late Golgi compartment protein 1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFridmann-Sirkis, Y. / Kent, H.M. / Lewis, M.J. / Evans, P.R. / Pelham, H.R.B.
CitationJournal: Traffic / Year: 2006
Title: Structural Analysis of the Interaction between the Snare Tlg1 and Vps51.
Authors: Fridmann-Sirkis, Y. / Kent, H.M. / Lewis, M.J. / Evans, P.R. / Pelham, H.R.B.
History
DepositionOct 27, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-SNARE AFFECTING A LATE GOLGI COMPARTMENT PROTEIN 1
B: T-SNARE AFFECTING A LATE GOLGI COMPARTMENT PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)22,4892
Polymers22,4892
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.666, 46.104, 117.887
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 T-SNARE AFFECTING A LATE GOLGI COMPARTMENT PROTEIN 1 / SYNTAXIN TLG1


Mass: 11244.396 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-95
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q03322
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.9 Å3/Da / Density % sol: 57.28 %
Crystal growpH: 5.6
Details: 20MG/ML PROTEIN, 8% PEG8000, 80MM K PHOSPHATE PH5.6, FROZEN IN 22.5% GLYCEROL, pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 30, 2004 / Details: OSMIC MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 14293 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.5 / % possible all: 91.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C5I

2c5i


Resolution: 2.1→58.93 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.882 / SU B: 6.062 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.311 725 5.1 %RANDOM
Rwork0.256 ---
obs0.259 13533 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--2.69 Å20 Å2
3----2.55 Å2
Refinement stepCycle: LAST / Resolution: 2.1→58.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1419 0 0 75 1494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221426
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.361.961913
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6215168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.312690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30115295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8511514
X-RAY DIFFRACTIONr_chiral_restr0.0950.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021078
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.2666
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.2999
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.259
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.041.5896
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58221388
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7893589
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4314.5525
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.401 61
Rwork0.277 907

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