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- PDB-1lvf: syntaxin 6 -

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Basic information

Entry
Database: PDB / ID: 1lvf
Titlesyntaxin 6
Componentssyntaxin 6
KeywordsTRANSPORT PROTEIN / SNARE / three-helix bundle
Function / homology
Function and homology information


regulation of protein localization => GO:0032880 / synaptic vesicle to endosome fusion / : / Intra-Golgi traffic / Retrograde transport at the Trans-Golgi-Network / Golgi ribbon formation / Golgi vesicle transport / vesicle fusion / vesicle docking / SNARE complex ...regulation of protein localization => GO:0032880 / synaptic vesicle to endosome fusion / : / Intra-Golgi traffic / Retrograde transport at the Trans-Golgi-Network / Golgi ribbon formation / Golgi vesicle transport / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / endosome organization / endocytic recycling / retrograde transport, endosome to Golgi / syntaxin binding / endomembrane system / phagocytic vesicle / vesicle-mediated transport / SNARE binding / trans-Golgi network membrane / intracellular protein transport / trans-Golgi network / terminal bouton / regulation of protein localization / synaptic vesicle / membrane => GO:0016020 / early endosome / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / membrane / cytosol
Similarity search - Function
Syntaxin 6, N-terminal / Syntaxin 6, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / SNARE domain / 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 ...Syntaxin 6, N-terminal / Syntaxin 6, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / SNARE domain / 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
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.1 Å
AuthorsMisura, K.M.S. / Bock, J.B. / Gonzalez, L.C. / Scheller, R.H. / Weis, W.I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Three-dimensional structure of the amino-terminal domain of syntaxin 6, a SNAP-25 C homolog.
Authors: Misura, K.M. / Bock, J.B. / Gonzalez Jr., L.C. / Scheller, R.H. / Weis, W.I.
History
DepositionMay 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: syntaxin 6
B: syntaxin 6


Theoretical massNumber of molelcules
Total (without water)25,3302
Polymers25,3302
Non-polymers00
Water3,711206
1
A: syntaxin 6


Theoretical massNumber of molelcules
Total (without water)12,6651
Polymers12,6651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: syntaxin 6


Theoretical massNumber of molelcules
Total (without water)12,6651
Polymers12,6651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.600, 54.380, 94.890
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 syntaxin 6 /


Mass: 12665.151 Da / Num. of mol.: 2 / Fragment: N-terminal domain (RESIDUES 1-110)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: Q63635
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 8000, sodium acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1150 mM1dropNaCl
25 mMbeta-mercaptoethanol1drop
310 mMHEPES1droppH7.4
430 %(v/v)PEG80001reservoir
5400 mMsodium acetate1reservoir
610 mMbeta-mercaptoethanol1reservoir
710 mMHEPES1reservoirpH7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1998 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→36.55 Å / Num. all: 12225 / Num. obs: 11792 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Biso Wilson estimate: 9.1 Å2 / Limit h max: 18 / Limit h min: 0 / Limit k max: 25 / Limit k min: 0 / Limit l max: 45 / Limit l min: 0 / Observed criterion F max: 1714937.98 / Observed criterion F min: 2.639
Reflection shellResolution: 2.1→2.19 Å / Redundancy: 3.9 % / Num. unique all: 11787 / Rsym value: 0.345 / % possible all: 96.7
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / % possible obs: 99.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.099
Reflection shell
*PLUS
% possible obs: 96.7 % / Rmerge(I) obs: 0.345

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Processing

Software
NameVersionClassification
SOLVEphasing
DMmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→36.55 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1217 10.3 %random
Rwork0.208 ---
all0.269 12500 --
obs0.208 11792 94.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 49.4386 Å2 / ksol: 0.35113 e/Å3
Displacement parametersBiso max: 55.04 Å2 / Biso mean: 22.1 Å2 / Biso min: 9.02 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å20 Å20 Å2
2--4.71 Å20 Å2
3----2.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.05 Å
Luzzati d res high-2.1
Refinement stepCycle: LAST / Resolution: 2.1→36.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 0 206 1898
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg0.9
X-RAY DIFFRACTIONx_torsion_deg15.2
X-RAY DIFFRACTIONx_torsion_impr_deg0.64
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.1-2.20.2191358.80.21612610.0191526139691.5
2.2-2.310.1881399.10.18512790.0161521141893.2
2.31-2.460.1961529.80.19813070.0161547145994.3
2.46-2.650.20215710.20.20413170.0161545147495.4
2.65-2.910.20413990.20413280.0171537146795.4
2.91-3.330.2216810.70.21813640.0171572153297.4
3.33-4.20.217310.90.19713550.0151591152896
4.2-36.550.2271549.20.22913640.0181673151890.7
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
Refinement
*PLUS
Num. reflection obs: 10571 / Num. reflection Rfree: 1216 / Rfactor all: 0.269 / Rfactor Rfree: 0.206 / Rfactor Rwork: 0.265
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 0.8728
LS refinement shell
*PLUS
Rfactor Rfree: 0.219 / Rfactor Rwork: 0.216

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