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

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Basic information

Entry
Database: PDB / ID: 4ikd
TitleCrystal structure of SNX11 PX domain
ComponentsSorting nexin-11
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: 1.6 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_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Sorting nexin-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4028
Polymers20,2041
Non-polymers1987
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.120, 62.400, 66.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sorting nexin-11


Mass: 20203.820 Da / Num. of mol.: 1 / Fragment: UNP residues 7-170
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: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
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: 2.05 Å3/Da / Density % sol: 39.89 % / Mosaicity: 0.28 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M HEPES pH 7.5, 20% PEG 8000, vapor diffusion, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.6→45.362 Å / Num. all: 22474 / Num. obs: 22474 / % possible obs: 99.7 % / Redundancy: 4.2 % / Rsym value: 0.123 / Net I/σ(I): 7.2
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
1.6-1.694.20.5980.5211.41382732540.2880.5980.5212.899.8
1.69-1.794.30.410.35821305630490.1960.410.3583.899.9
1.79-1.914.30.2630.233.11238228910.1260.2630.235.3100
1.91-2.074.30.1850.1614.11151026890.0880.1850.161799.9
2.07-2.264.30.1540.1344.51060724950.0740.1540.1348.5100
2.26-2.534.20.1390.1214.9960722700.0670.1390.1219.5100
2.53-2.924.20.1370.124.6839920160.0660.1370.1210.399.9
2.92-3.584.10.1360.1194.5694416930.0650.1360.11911.299
3.58-5.063.90.1150.0995.6524113560.0570.1150.09911.698.9
5.06-34.2913.80.120.1025.228717610.0610.120.10211.395

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→34.29 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.2509 / WRfactor Rwork: 0.2013 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8703 / SU B: 1.636 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0925 / SU Rfree: 0.1008 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2374 1142 5.1 %RANDOM
Rwork0.186 ---
obs0.1885 22322 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.68 Å2 / Biso mean: 24.3801 Å2 / Biso min: 9.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2--0.76 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1214 0 7 158 1379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191299
X-RAY DIFFRACTIONr_bond_other_d0.0010.02910
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.9781771
X-RAY DIFFRACTIONr_angle_other_deg0.96532212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8355167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.18323.18266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09515216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0371514
X-RAY DIFFRACTIONr_chiral_restr0.1120.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02283
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 66 -
Rwork0.276 1425 -
all-1491 -
obs--99.67 %

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