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- PDB-4ikb: Crystal structure of SNX11 PX domain -

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Basic information

Entry
Database: PDB / ID: 4ikb
TitleCrystal structure of SNX11 PX domain
Components(Sorting nexin- ...) x 2
KeywordsPROTEIN TRANSPORT / SNX11 / PX domain
Function / homology
Function and homology information


phosphatidylinositol phosphate binding / vesicle organization / intracellular protein transport / endosome / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsXu, J. / Xu, T. / Liu, J.
CitationJournal: to be published
Title: Structure of Sorting Nexin 11 (SNX11) Reveals a Novel Extended PX Domain (PXe Domain) Critical for the Inhibition of Sorting Nexin 10 (SNX10) Induced Vacuolation
Authors: Xu, J. / Xu, T. / Liu, J.
History
DepositionDec 26, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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-11
B: Sorting nexin-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,18220
Polymers34,2682
Non-polymers2,91318
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-128 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.480, 38.740, 73.460
Angle α, β, γ (deg.)90.000, 101.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Sorting nexin- ... , 2 types, 2 molecules AB

#1: Protein Sorting nexin-11


Mass: 17156.113 Da / Num. of mol.: 1 / Fragment: PX domain, UNP residues 7-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5W9
#2: Protein Sorting nexin-11


Mass: 17112.248 Da / Num. of mol.: 1 / Fragment: PX domain, UNP residues 7-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5W9

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Non-polymers , 5 types, 265 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: 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.: 5 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.55 % / Mosaicity: 0.22 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.2M ammonium sulfate, 0.1M Sodium cacodylate trihydrate pH 6.5, 30% PEG 8000, vapor diffusion, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.776→72.069 Å / Num. all: 27836 / Num. obs: 27836 / % possible obs: 97.4 % / Redundancy: 5.2 % / Rsym value: 0.064 / Net I/σ(I): 17.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.78-1.885.30.1440.1295.22100539730.0630.1440.1299.896.4
1.88-1.995.30.1110.0996.81993237740.0490.1110.09912.496.5
1.99-2.135.30.0890.088.51904335990.0390.0890.0815.197.1
2.13-2.35.30.0770.0698.81761033400.0340.0770.06917.597.4
2.3-2.525.30.0720.06510.11627030950.0320.0720.0651997.8
2.52-2.815.20.0690.06210.41473728130.030.0690.06220.798.1
2.81-3.255.20.0680.06110.11313825130.0290.0680.0612398.6
3.25-3.985.20.0650.05810.31100221290.0290.0650.05825.198.9
3.98-5.6350.0650.05810.6852416940.0290.0650.05825.399.2
5.63-34.1164.60.0660.05910.741739060.0310.0660.0592394.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→34.12 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2406 / WRfactor Rwork: 0.1833 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.867 / SU B: 2.267 / SU ML: 0.074 / SU R Cruickshank DPI: 0.1192 / SU Rfree: 0.1238 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 1407 5.1 %RANDOM
Rwork0.1687 ---
obs0.1713 27834 97.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.04 Å2 / Biso mean: 19.4674 Å2 / Biso min: 6.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20.27 Å2
2---0.09 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.78→34.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 78 247 2436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192258
X-RAY DIFFRACTIONr_bond_other_d0.0070.021584
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.983051
X-RAY DIFFRACTIONr_angle_other_deg0.94233840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0965268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79423.125112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33215393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5181522
X-RAY DIFFRACTIONr_chiral_restr0.130.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022417
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02481
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 92 -
Rwork0.185 1823 -
all-1915 -
obs--95.56 %

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