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- PDB-2ett: Solution Structure of Human Sorting Nexin 22 PX Domain -

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Basic information

Entry
Database: PDB / ID: 2ett
TitleSolution Structure of Human Sorting Nexin 22 PX Domain
ComponentsSorting nexin-22
KeywordsPROTEIN TRANSPORT / PX domain / sorting nexin 22 / BC019655 / SNX22_HUMAN / Hs.157607 / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG
Function / homology
Function and homology information


phosphatidylinositol phosphate binding / cytoplasmic vesicle membrane / protein transport
Similarity search - Function
: / 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)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS FOR INITIAL STRUCTURE CALCULATION, MOLECULAR DYNAMICS, SIMULATED ANNEALING FOR FINAL STRUCTURE REFINEMENT
AuthorsSong, J. / Zhao, Q. / Tyler, R.C. / Lee, M.S. / Newman, C.L. / Markley, J.L. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Protein Sci. / Year: 2007
Title: Solution structure of human sorting nexin 22.
Authors: Song, J. / Zhao, K.Q. / Newman, C.L. / Vinarov, D.A. / Markley, J.L.
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sorting nexin-22


Theoretical massNumber of molelcules
Total (without water)15,2191
Polymers15,2191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Sorting nexin-22


Mass: 15219.476 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: WHEAT GERM CELL-FREE, IN VITRO EXPRESSION / Gene: SNX22 / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: Q96L94

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H,15N-HSQC
1211H,13C-HSQC
131HN(CA)CB
141CBCA(CO)NH
151C(CO)NH
161H(CCO)NH
171HBACONH
181HNHA
191HNCA
1101HN(CO)CA
1111HNCO
1121(H)CCH-TOCSY
113113C-edited 1H,1H-NOESY
114115N-edited 1H,1H-NOESY
NMR detailsText: ALL TRIPLE-RESONANCE AND NOESY SPECTRA WERE ACQUIRED USING A CRYOGENIC PROBE.

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Sample preparation

DetailsContents: 0.5 MM 13C,15N-LABELED BC019655, 10 MM BIS-TRIS, 100 MM NACL, 10 MM DTT, 50 MM ARGININE HYDROCHLORIDE, 50 MM SODIUM GLUTAMATE, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 202 mM / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
XPLOR-NIH 2.9.3.G. Marius Clore, John Kuszewski, Charles D. Schwieters, Nico Tjandra.refinement
VNMR 1.1structure solution
NMRPIPE 97.027.12.56.structure solution
SPARKY 3.72structure solution
CYANA 2.1structure solution
XPLOR-NIH 2.9.3.structure solution
RefinementMethod: TORSION ANGLE DYNAMICS FOR INITIAL STRUCTURE CALCULATION, MOLECULAR DYNAMICS, SIMULATED ANNEALING FOR FINAL STRUCTURE REFINEMENT
Software ordinal: 1
Details: STRUCTURES ARE BASED ON A TOTAL OF 1885 NOE RESTRAINTS (801 INTRA, 449 SEQUENTIAL, 277 MEDIUM, AND 358 LONG RANGE), 76 HBOND RESTRAINTS, AND 172 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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