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- PDB-6ecm: Crystal Structure of SNX15 PX domain in domain swapped conformation -

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Basic information

Entry
Database: PDB / ID: 6ecm
TitleCrystal Structure of SNX15 PX domain in domain swapped conformation
ComponentsSorting nexin-15
KeywordsLIPID BINDING PROTEIN / PX domain / endosome / trafficking / sorting nexin
Function / homology
Function and homology information


phosphatidylinositol binding / cytoplasmic vesicle membrane / intracellular protein transport / intracellular membrane-bounded organelle / nucleolus / membrane / plasma membrane / cytosol
Similarity search - Function
: / MIT (microtubule interacting and transport) domain / MIT domain superfamily / MIT domain / Microtubule Interacting and Trafficking molecule domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.353 Å
AuthorsChandra, M. / Collins, B.M.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP160101743 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1099114 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1136021 Australia
CitationJournal: Nat Commun / Year: 2019
Title: Classification of the human phox homology (PX) domains based on their phosphoinositide binding specificities.
Authors: Chandra, M. / Chin, Y.K. / Mas, C. / Feathers, J.R. / Paul, B. / Datta, S. / Chen, K.E. / Jia, X. / Yang, Z. / Norwood, S.J. / Mohanty, B. / Bugarcic, A. / Teasdale, R.D. / Henne, W.M. / ...Authors: Chandra, M. / Chin, Y.K. / Mas, C. / Feathers, J.R. / Paul, B. / Datta, S. / Chen, K.E. / Jia, X. / Yang, Z. / Norwood, S.J. / Mohanty, B. / Bugarcic, A. / Teasdale, R.D. / Henne, W.M. / Mobli, M. / Collins, B.M.
History
DepositionAug 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2302
Polymers15,1341
Non-polymers961
Water1629
1
A: Sorting nexin-15
hetero molecules

A: Sorting nexin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4604
Polymers30,2682
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2280 Å2
ΔGint-50 kcal/mol
Surface area12450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.498, 54.498, 83.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Sorting nexin-15


Mass: 15134.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NRS6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 40.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris (pH 8.5) 200 mM LiSO4, 24% PEG4000, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.35→45 Å / Num. obs: 5645 / % possible obs: 99.4 % / Redundancy: 26.2 % / CC1/2: 1 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.015 / Net I/σ(I): 20.9
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 24.6 % / Rmerge(I) obs: 1.074 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 505 / CC1/2: 0.982 / Rpim(I) all: 0.216 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IKD

4ikd


Resolution: 2.353→45 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.43
RfactorNum. reflection% reflection
Rfree0.2989 560 10.06 %
Rwork0.2443 --
obs0.2499 5569 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.353→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms829 0 5 9 843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006853
X-RAY DIFFRACTIONf_angle_d1.0361147
X-RAY DIFFRACTIONf_dihedral_angle_d15.001318
X-RAY DIFFRACTIONf_chiral_restr0.038120
X-RAY DIFFRACTIONf_plane_restr0.005145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.353-2.58970.36361340.2941197X-RAY DIFFRACTION97
2.5897-2.96440.3971370.29241219X-RAY DIFFRACTION99
2.9644-3.73460.33641380.26241239X-RAY DIFFRACTION99
3.7346-45.65930.26351510.22331354X-RAY DIFFRACTION100

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