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- PDB-4p2i: Crystal structure of the mouse SNX19 PX domain -

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Basic information

Entry
Database: PDB / ID: 4p2i
TitleCrystal structure of the mouse SNX19 PX domain
ComponentsMKIAA0254 protein
KeywordsSIGNALING PROTEIN / sorting nexin / phox homology domain
Function / homology
Function and homology information


dense core granule maturation / insulin secretion / exocytosis / chondrocyte differentiation / phosphatidylinositol binding / establishment of localization in cell / early endosome membrane / intracellular membrane-bounded organelle
Similarity search - Function
SNX19, PX domain / Phox-associated domain / Sorting nexin, C-terminal / PXA domain / Sorting nexin C terminal / PXA domain profile. / Domain associated with PX domains / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. ...SNX19, PX domain / Phox-associated domain / Sorting nexin, C-terminal / PXA domain / Sorting nexin C terminal / PXA domain profile. / Domain associated with PX domains / 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
Sorting nexin-19 / Sorting nexin-19
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsCollins, B.M.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT100100027 Australia
Australian Research Council (ARC)DP0985029 Australia
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Basis for Different Phosphoinositide Specificities of the PX Domains of Sorting Nexins Regulating G-protein Signaling.
Authors: Mas, C. / Norwood, S.J. / Bugarcic, A. / Kinna, G. / Leneva, N. / Kovtun, O. / Ghai, R. / Ona Yanez, L.E. / Davis, J.L. / Teasdale, R.D. / Collins, B.M.
History
DepositionMar 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Jan 17, 2018Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MKIAA0254 protein
B: MKIAA0254 protein


Theoretical massNumber of molelcules
Total (without water)31,3182
Polymers31,3182
Non-polymers00
Water5,567309
1
A: MKIAA0254 protein


Theoretical massNumber of molelcules
Total (without water)15,6591
Polymers15,6591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MKIAA0254 protein


Theoretical massNumber of molelcules
Total (without water)15,6591
Polymers15,6591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.840, 32.938, 81.966
Angle α, β, γ (deg.)90.00, 107.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MKIAA0254 protein


Mass: 15658.753 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Snx19, mKIAA0254 / Production host: Escherichia coli (E. coli) / References: UniProt: Q80U53, UniProt: Q6P4T1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG3350, 0.25 M NaCl, 5% glycerol, 0.1 M Tris (pH 8)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray / Wavelength: 0.9537
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→31.7 Å / Num. obs: 26154 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 15.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.1_357) / Classification: refinement
RefinementResolution: 1.9→30.44 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 23.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 1300 5.07 %
Rwork0.2114 --
obs0.2133 25639 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.993 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.7376 Å2-0 Å20.0344 Å2
2---2.7353 Å20 Å2
3----2.0022 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 0 309 2205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071926
X-RAY DIFFRACTIONf_angle_d0.9832592
X-RAY DIFFRACTIONf_dihedral_angle_d14.252742
X-RAY DIFFRACTIONf_chiral_restr0.071295
X-RAY DIFFRACTIONf_plane_restr0.004331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9760.27341160.24582564X-RAY DIFFRACTION94
1.976-2.06590.2761410.21482700X-RAY DIFFRACTION97
2.0659-2.17480.27191480.2162665X-RAY DIFFRACTION98
2.1748-2.31110.25261400.20852662X-RAY DIFFRACTION98
2.3111-2.48940.25131320.21712718X-RAY DIFFRACTION98
2.4894-2.73980.26051430.22232718X-RAY DIFFRACTION98
2.7398-3.13590.25891560.21482694X-RAY DIFFRACTION99
3.1359-3.94950.21071520.18822775X-RAY DIFFRACTION100
3.9495-30.44390.23991720.20632843X-RAY DIFFRACTION99

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