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- PDB-4on3: Crystal structure of human sorting nexin 10 (SNX10) -

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Basic information

Entry
Database: PDB / ID: 4on3
TitleCrystal structure of human sorting nexin 10 (SNX10)
ComponentsSorting nexin-10
KeywordsPROTEIN TRANSPORT / sorting nexin / phox-homology domain
Function / homology
Function and homology information


extrinsic component of endosome membrane / apical cytoplasm / tooth eruption / gastric acid secretion / 1-phosphatidylinositol binding / phosphatidylinositol phosphate binding / bone mineralization involved in bone maturation / vesicle organization / ruffle assembly / endosome organization ...extrinsic component of endosome membrane / apical cytoplasm / tooth eruption / gastric acid secretion / 1-phosphatidylinositol binding / phosphatidylinositol phosphate binding / bone mineralization involved in bone maturation / vesicle organization / ruffle assembly / endosome organization / protein localization to cilium / cellular homeostasis / protein localization to centrosome / cilium assembly / bone resorption / calcium ion homeostasis / osteoclast differentiation / secretory granule / cellular response to leukemia inhibitory factor / intracellular protein transport / endocytosis / ATPase binding / endosome / centrosome / endoplasmic reticulum / nucleus
Similarity search - Function
Sorting nexin-10/11 / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Sorting nexin-10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsXu, T. / Xu, J. / Wang, Q. / Liu, J.
CitationJournal: Proteins / Year: 2014
Title: Structure of human SNX10 reveals insights into its role in human autosomal recessive osteopetrosis.
Authors: Xu, T. / Xu, J. / Ye, Y. / Wang, Q. / Shu, X. / Pei, D. / Liu, J.
History
DepositionJan 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sorting nexin-10
B: Sorting nexin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,77434
Polymers49,3392
Non-polymers3,43532
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-84 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.130, 205.130, 42.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-302-

NO3

21A-302-

NO3

31A-314-

NA

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Components

#1: Protein Sorting nexin-10


Mass: 24669.418 Da / Num. of mol.: 2 / Fragment: C42A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5X0
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 5.2 Å3/Da / Density % sol: 76.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 4 M sodium nitrate, 0.1 M BIS-TRIS propane pH 7.0, vapor diffusion, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.55→67.14 Å / Num. obs: 32565 / % possible obs: 98 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.55-2.662.70.0121.2195.6
8.83-67.143.40.01221.7198.2

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Processing

Software
NameVersionClassificationNB
Aimless0.2.14data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→67.145 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.894 / SU B: 7.504 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22912 1471 4.8 %RANDOM
Rwork0.18918 ---
obs0.1911 29361 78.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.298 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0.24 Å20 Å2
2---0.48 Å20 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.6→67.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2547 0 144 24 2715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192719
X-RAY DIFFRACTIONr_bond_other_d0.0020.022565
X-RAY DIFFRACTIONr_angle_refined_deg2.181.963618
X-RAY DIFFRACTIONr_angle_other_deg0.9835863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1515299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42123.154149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.86715476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3111528
X-RAY DIFFRACTIONr_chiral_restr0.1240.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023009
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02695
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8952.4821202
X-RAY DIFFRACTIONr_mcbond_other2.8962.4771201
X-RAY DIFFRACTIONr_mcangle_it53.7011499
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8683.1691517
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 6 -
Rwork0.282 252 -
obs--11.11 %

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