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- PDB-6kok: Crystal Structure of SNX11/SNX10-PXe Chimera -

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Basic information

Entry
Database: PDB / ID: 6kok
TitleCrystal Structure of SNX11/SNX10-PXe Chimera
ComponentsSorting nexin-11,Uncharacterized protein SNX10
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 / ruffle assembly / vesicle organization / 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 / ruffle assembly / vesicle organization / 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 / membrane / plasma membrane / cytoplasm
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
Uncharacterized protein SNX10 / Sorting nexin-11 / Sorting nexin-10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsXu, T. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31570759 China
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Molecular Basis for PI(3,5)P2Recognition by SNX11, a Protein Involved in Lysosomal Degradation and Endosome Homeostasis Regulation.
Authors: Xu, T. / Gan, Q. / Wu, B. / Yin, M. / Xu, J. / Shu, X. / Liu, J.
History
DepositionAug 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sorting nexin-11,Uncharacterized protein SNX10
B: Sorting nexin-11,Uncharacterized protein SNX10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,97216
Polymers37,4882
Non-polymers48414
Water3,729207
1
A: Sorting nexin-11,Uncharacterized protein SNX10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0289
Polymers18,7441
Non-polymers2848
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area9360 Å2
MethodPISA
2
B: Sorting nexin-11,Uncharacterized protein SNX10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9447
Polymers18,7441
Non-polymers2006
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.103, 47.910, 87.309
Angle α, β, γ (deg.)90.000, 94.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sorting nexin-11,Uncharacterized protein SNX10


Mass: 18744.201 Da / Num. of mol.: 2 / Fragment: SNX11/SNX10-PXe Chimera
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Homo sapiens (human) / Gene: SNX11, SNX10 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2
References: UniProt: Q9Y5W9, UniProt: Q75MY3, UniProt: Q9Y5X0*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.23 Å3/Da / Density % sol: 44.86 % / Mosaicity: 0.77 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6 / Details: 2.2 M NaCl, 0.1 M NaAc pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2→47.91 Å / Num. obs: 21816 / % possible obs: 97 % / Redundancy: 3.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.044 / Rrim(I) all: 0.085 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.053.60.125570015850.9710.0750.1477.697.6
8.95-47.913.70.05910272800.9870.0360.06915.799

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IKB

4ikb


Resolution: 2→43.53 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2497 1963 4.75 %RANDOM
Rwork0.2043 39328 --
obs0.2065 21780 94.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.43 Å2 / Biso mean: 10.0853 Å2 / Biso min: 0.02 Å2
Refinement stepCycle: final / Resolution: 2→43.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2427 0 14 207 2648
Biso mean--14.49 14.44 -
Num. residues----295
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.050.27821270.2181276795
2.05-2.110.26991530.2111293397
2.11-2.170.32941340.2092291497
2.17-2.240.23831270.212287495
2.24-2.320.30811490.2202280295
2.32-2.410.29831360.2043282996
2.41-2.520.28951500.2175288095
2.52-2.650.23011410.2123273193
2.65-2.820.23851490.224250384
2.82-3.040.26211090.2103280294
3.04-3.340.24081770.2082287097
3.34-3.830.22621510.1752281296
3.83-4.820.20211450.1725277793
4.82-43.530.20591150.2059283494

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