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- PDB-3lui: Crystal structure of the SNX17 PX domain with bound sulphate -

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Basic information

Entry
Database: PDB / ID: 3lui
TitleCrystal structure of the SNX17 PX domain with bound sulphate
ComponentsSorting nexin-17
KeywordsPROTEIN TRANSPORT / SNX17 / sorting nexin / PX domain / endosome / Phosphoprotein / Transport
Function / homology
Function and homology information


cardiac septum development / endocytic recycling / coronary vasculature development / cholesterol catabolic process / aorta development / endosomal transport / low-density lipoprotein particle receptor binding / regulation of endocytosis / phosphatidylinositol binding / receptor-mediated endocytosis ...cardiac septum development / endocytic recycling / coronary vasculature development / cholesterol catabolic process / aorta development / endosomal transport / low-density lipoprotein particle receptor binding / regulation of endocytosis / phosphatidylinositol binding / receptor-mediated endocytosis / kidney development / intracellular protein transport / cytoplasmic vesicle / early endosome / endosome / endosome membrane / signaling receptor binding / intracellular membrane-bounded organelle / Golgi apparatus / signal transduction / protein-containing complex / membrane / cytosol
Similarity search - Function
Sorting nexin-17 / SNX17, atypical FERM-like domain / Sorting nexin-17/31, FERM domain / : / : / Sorting Nexin 17 FERM C-terminal domain / Sortin nexin 17/31, FERM domain, F2 lobe / Sortin nexin 17/27/31, FERM domain, F1 lobe / Phox-like domain / PX Domain ...Sorting nexin-17 / SNX17, atypical FERM-like domain / Sorting nexin-17/31, FERM domain / : / : / Sorting Nexin 17 FERM C-terminal domain / Sortin nexin 17/31, FERM domain, F2 lobe / Sortin nexin 17/27/31, FERM domain, F1 lobe / Phox-like domain / PX Domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / PH-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGhai, R. / Collins, B.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Phox homology band 4.1/ezrin/radixin/moesin-like proteins function as molecular scaffolds that interact with cargo receptors and Ras GTPases
Authors: Ghai, R. / Mobli, M. / Norwood, S.J. / Bugarcic, A. / Teasdale, R.D. / King, G.F. / Collins, B.M.
History
DepositionFeb 17, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sorting nexin-17
B: Sorting nexin-17
C: Sorting nexin-17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8249
Polymers39,2483
Non-polymers5766
Water9,368520
1
A: Sorting nexin-17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2753
Polymers13,0831
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sorting nexin-17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3714
Polymers13,0831
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sorting nexin-17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1792
Polymers13,0831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.893, 66.588, 98.193
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 Sorting nexin-17 / SNX17


Mass: 13082.650 Da / Num. of mol.: 3 / Fragment: SNX17 PX domain (residues 1-112)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX17 / Plasmid: pET based ligation-independent vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15036
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.8M lithium sulphate, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.541 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.8→55.1 Å / Num. obs: 34117 / % possible obs: 96.5 % / Observed criterion σ(I): 2.1 / Redundancy: 2.1 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 12.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.52 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.1 / % possible all: 96.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.227 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.825 / SU ML: 0.26 / σ(F): 0.02 / Phase error: 24.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2447 1640 5.01 %
Rwork0.2002 --
obs0.2025 32750 92.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.969 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso max: 63.17 Å2 / Biso mean: 25.733 Å2 / Biso min: 9.33 Å2
Baniso -1Baniso -2Baniso -3
1--2.294 Å2-0 Å20 Å2
2---1.784 Å2-0 Å2
3---4.078 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2594 0 30 520 3144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062672
X-RAY DIFFRACTIONf_angle_d0.9173605
X-RAY DIFFRACTIONf_dihedral_angle_d16.459999
X-RAY DIFFRACTIONf_chiral_restr0.064379
X-RAY DIFFRACTIONf_plane_restr0.004473
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8640.3071320.2532779291184
1.864-1.9390.3051520.2392888304088
1.939-2.0270.3051690.2273065323492
2.027-2.1340.2531430.1993130327394
2.134-2.2680.2481700.1943027319792
2.268-2.4430.2641930.1953142333595
2.443-2.6890.2611790.2023259343897
2.689-3.0780.2561600.2093314347498
3.078-3.8770.2121400.1693222336294
3.877-49.2450.2132020.1883284348693

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