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- PDB-4dnd: Crystal structure of syntaxin 10 from Homo sapiens -

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Basic information

Entry
Database: PDB / ID: 4dnd
TitleCrystal structure of syntaxin 10 from Homo sapiens
ComponentsSyntaxin-10
KeywordsTRANSPORT PROTEIN / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


: / Retrograde transport at the Trans-Golgi-Network / Golgi vesicle transport / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / retrograde transport, endosome to Golgi / syntaxin binding / endomembrane system ...: / Retrograde transport at the Trans-Golgi-Network / Golgi vesicle transport / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / retrograde transport, endosome to Golgi / syntaxin binding / endomembrane system / SNARE binding / trans-Golgi network membrane / intracellular protein transport / trans-Golgi network / regulation of protein localization / synaptic vesicle / vesicle / membrane => GO:0016020 / perinuclear region of cytoplasm / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Seidel, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of syntaxin 10 from Homo sapiens
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Seidel, R. / Almo, S.C.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Syntaxin-10


Theoretical massNumber of molelcules
Total (without water)15,3181
Polymers15,3181
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)22.186, 58.733, 36.518
Angle α, β, γ (deg.)90.000, 100.210, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Syntaxin-10 / / Syn10


Mass: 15318.346 Da / Num. of mol.: 1 / Fragment: Cytoplasmic Topological domain residues 1-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: Bronx / Gene: AAC05087.1, STX10, SYN10 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: O60499
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 1.56 Å3/Da / Density % sol: 21.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG400, 0.1M Tris pH 8.5, 0.2M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 2.8 % / Av σ(I) over netI: 31.76 / Number: 95400 / Rmerge(I) obs: 0.046 / Χ2: 1.46 / D res high: 1.4 Å / D res low: 50 Å / Num. obs: 33753 / % possible obs: 94.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.85070.210.0383.3442.6
3.023.884.810.0352.9982.6
2.633.0297.410.0362.7542.8
2.392.6398.910.0392.6432.8
2.222.399910.042.1852.9
2.092.2298.810.0391.7462.9
1.992.0998.110.0451.622.9
1.91.9998.110.0491.3032.9
1.831.99810.0661.2252.9
1.761.839810.0771.1052.9
1.711.7697.610.0911.0542.9
1.661.7196.710.111.0512.9
1.621.6696.510.1130.9552.9
1.581.6297.510.1420.9382.9
1.541.5896.610.1830.9022.9
1.511.5495.910.1980.8562.9
1.481.5196.310.250.9112.9
1.451.4895.110.3340.832.8
1.421.4592.310.3780.792.7
1.41.4275.610.5110.7972.5
ReflectionResolution: 1.4→50 Å / Num. obs: 18149 / % possible obs: 94.1 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.046 / Χ2: 1.46 / Net I/σ(I): 14.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.4-1.422.50.51113020.797175.6
1.42-1.452.70.37816750.79192.3
1.45-1.482.80.33417580.83195.1
1.48-1.512.90.2517070.911196.3
1.51-1.542.90.19816870.856195.9
1.54-1.582.90.18317840.902196.6
1.58-1.622.90.14216940.938197.5
1.62-1.662.90.11317350.955196.5
1.66-1.712.90.1117951.051196.7
1.71-1.762.90.09116921.054197.6
1.76-1.832.90.07717971.105198
1.83-1.92.90.06617331.225198
1.9-1.992.90.04917701.303198.1
1.99-2.092.90.04517671.62198.1
2.09-2.222.90.03917851.746198.8
2.22-2.392.90.0417612.185199
2.39-2.632.80.03917662.643198.9
2.63-3.022.80.03617562.754197.4
3.02-3.82.60.03515172.998184.8
3.8-502.60.03812723.344170.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→17.52 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.2122 / WRfactor Rwork: 0.1692 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8781 / SU B: 2.4 / SU ML: 0.043 / SU R Cruickshank DPI: 0.0799 / SU Rfree: 0.0706 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1996 879 5.1 %RANDOM
Rwork0.162 ---
obs0.1638 17283 95.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.31 Å2 / Biso mean: 22.7954 Å2 / Biso min: 10.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.4→17.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms782 0 0 120 902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.019805
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.971085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.721596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72724.44445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52815140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.567158
X-RAY DIFFRACTIONr_chiral_restr0.0670.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021612
X-RAY DIFFRACTIONr_rigid_bond_restr2.9873805
X-RAY DIFFRACTIONr_sphericity_free18.6537
X-RAY DIFFRACTIONr_sphericity_bonded10.6945873
LS refinement shellResolution: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 76 -
Rwork0.229 1108 -
all-1184 -
obs--91.57 %
Refinement TLS params.Method: refined / Origin x: -0.1801 Å / Origin y: -0.641 Å / Origin z: 11.2748 Å
111213212223313233
T0.0158 Å20.0004 Å20.0027 Å2-0.0007 Å2-0.0009 Å2--0.0153 Å2
L0.6851 °2-0.2986 °2-0.5812 °2-0.7334 °20.6664 °2--1.1041 °2
S-0.0089 Å °0.0032 Å °0.0038 Å °-0.0116 Å °0.0091 Å °-0.001 Å °0.0275 Å °-0.0043 Å °-0.0003 Å °

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