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- PDB-4ymr: Crystal structure of the domain swapped PXB/TPR domain of mouse SNX21 -

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Basic information

Entry
Database: PDB / ID: 4ymr
TitleCrystal structure of the domain swapped PXB/TPR domain of mouse SNX21
ComponentsProtein Snx21
KeywordsPROTEIN TRANSPORT / tetratricopeptide repeat endosome trafficking
Function / homology
Function and homology information


phosphatidylinositol-3-phosphate binding / phosphatidylinositol-4,5-bisphosphate binding / cytoplasmic vesicle membrane / protein transport / early endosome membrane
Similarity search - Function
Sorting nexin SNX20/SNX21 / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsCollins, B.C. / Teasdale, R.D. / Clairfeuille, T.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structure and Membrane Binding Properties of the Endosomal Tetratricopeptide Repeat (TPR) Domain-containing Sorting Nexins SNX20 and SNX21.
Authors: Clairfeuille, T. / Norwood, S.J. / Qi, X. / Teasdale, R.D. / Collins, B.M.
History
DepositionMar 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Protein Snx21
B: Protein Snx21


Theoretical massNumber of molelcules
Total (without water)32,0632
Polymers32,0632
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-34 kcal/mol
Surface area14100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.920, 100.920, 63.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Protein Snx21


Mass: 16031.377 Da / Num. of mol.: 2 / Fragment: residues 230-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Snx21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3UR97
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.1 M MES/imidazole (pH 6.5) 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium l-tartrate, 0.02 M sodium oxamate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→21.5 Å / Num. obs: 13890 / % possible obs: 93 % / Redundancy: 4.4 % / Net I/σ(I): 10.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.2_869)refinement
Aimlessdata scaling
RefinementResolution: 2.4→21.487 Å / SU ML: 0.8 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.17 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2672 692 4.99 %
Rwork0.2279 --
obs0.2298 13873 93.11 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.3 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.0691 Å2-0 Å2-0 Å2
2--2.0691 Å20 Å2
3----4.1383 Å2
Refinement stepCycle: LAST / Resolution: 2.4→21.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 0 21 2069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082090
X-RAY DIFFRACTIONf_angle_d1.3682843
X-RAY DIFFRACTIONf_dihedral_angle_d18.616795
X-RAY DIFFRACTIONf_chiral_restr0.085326
X-RAY DIFFRACTIONf_plane_restr0.012371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.58530.33261230.29541932X-RAY DIFFRACTION70
2.5853-2.84490.32591580.26182658X-RAY DIFFRACTION96
2.8449-3.25540.32311340.26692809X-RAY DIFFRACTION100
3.2554-4.09680.25871380.22842849X-RAY DIFFRACTION100
4.0968-21.48830.21851390.1932933X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 73.4759 Å / Origin y: 45.8617 Å / Origin z: 5.5007 Å
111213212223313233
T0.1409 Å2-0.0435 Å2-0.0284 Å2-0.3025 Å20.0493 Å2--0.1611 Å2
L2.9133 °21.299 °2-0.8032 °2-1.0376 °2-0.6117 °2--0.6783 °2
S-0.1136 Å °0.4242 Å °0.2251 Å °0.0192 Å °0.0406 Å °0.0462 Å °-0.0852 Å °0.0224 Å °0.0391 Å °
Refinement TLS groupSelection details: all

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