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

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Basic information

Entry
Database: PDB / ID: 4pzg
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 / cellular homeostasis / protein localization to cilium / 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: 2.8 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
DepositionMar 30, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,87420
Polymers49,4032
Non-polymers3,47118
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint0 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.859, 205.859, 42.330
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-302-

NO3

21A-302-

NO3

31A-305-

NO3

41A-305-

NO3

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A8 - 156
2010B8 - 156

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Components

#1: Protein Sorting nexin-10


Mass: 24701.484 Da / Num. of mol.: 2
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.: 11 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL, POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 5.24 Å3/Da / Density % sol: 76.53 %
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: Mar 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→49.45 Å / Num. obs: 25144 / % possible obs: 98.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 10.5 / Scaling rejects: 121
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.8-2.953.80.6742.213007346594.6
8.85-49.4510.50.04327.2898285699.5

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Processing

Software
NameVersionClassificationNB
Aimless0.1.29data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49.45 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.894 / SU B: 8.622 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1277 5.1 %RANDOM
Rwork0.1944 ---
obs0.1966 25133 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 152.81 Å2 / Biso mean: 42.045 Å2 / Biso min: 10.03 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å21.14 Å20 Å2
2--1.14 Å20 Å2
3----3.69 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2558 0 87 15 2660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192687
X-RAY DIFFRACTIONr_bond_other_d0.0060.022531
X-RAY DIFFRACTIONr_angle_refined_deg1.971.953592
X-RAY DIFFRACTIONr_angle_other_deg1.2553.0015778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3875300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4723.2150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.94215480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8861528
X-RAY DIFFRACTIONr_chiral_restr0.1020.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023008
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02696
Refine LS restraints NCS

Ens-ID: 1 / Number: 8806 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 102 -
Rwork0.34 1612 -
all-1714 -
obs--92.5 %

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