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- PDB-3iq2: Human sorting nexin 7, phox homology (PX) domain -

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Basic information

Entry
Database: PDB / ID: 3iq2
TitleHuman sorting nexin 7, phox homology (PX) domain
ComponentsSorting nexin-7
KeywordsPROTEIN TRANSPORT / SORTING NEXIN / SNX7 / PHOX / PROTEIN SIGNALLING / SGC / STRUCTURAL GENOMICS CONSORTIUM / Transport
Function / homology
Function and homology information


positive regulation of autophagosome assembly / piecemeal microautophagy of the nucleus / endocytic recycling / phagophore assembly site / reticulophagy / autophagy of mitochondrion / phosphatidylinositol binding / protein transport / early endosome membrane / early endosome
Similarity search - Function
SNX7, PX domain / SNX7, BAR domain / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily ...SNX7, PX domain / SNX7, BAR domain / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKarlberg, T. / Wisniewska, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Karlberg, T. / Wisniewska, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kallas, A. / Kotenyova, T. / Kotzsch, A. / Kraulis, P. / Nielsen, T.K. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Roos, A.K. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Schuler, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human Sorting Nexin 7, Phox Homology (Px) Domain
Authors: Karlberg, T. / Wisniewska, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / ...Authors: Karlberg, T. / Wisniewska, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kallas, A. / Kotenyova, T. / Kotzsch, A. / Kraulis, P. / Moche, M. / Nielsen, T.K. / Nordlund, P. / Nyman, T. / Persson, C. / Roos, A.K. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Schuler, H.
History
DepositionAug 19, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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-7
B: Sorting nexin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,26215
Polymers33,0212
Non-polymers1,24113
Water7,116395
1
A: Sorting nexin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1798
Polymers16,5111
Non-polymers6687
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sorting nexin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0837
Polymers16,5111
Non-polymers5726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.300, 57.300, 97.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Sorting nexin-7


Mass: 16510.701 Da / Num. of mol.: 2 / Fragment: PX-DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX7 / Plasmid: pNIC-CH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: Q9UNH6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.77 Å3/Da / Density % sol: 55.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2M AmmoniumSulfate, 0.1M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 12, 2009 / Details: Multilayer mirror
RadiationMonochromator: Bent Si (111) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0379 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 39129 / Num. obs: 39129 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.087 / Rsym value: 0.143 / Net I/σ(I): 13.1
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.8 / Num. unique all: 6200 / Rsym value: 0.636 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.5.0035refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OCS

1ocs


Resolution: 1.7→28.65 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.652 / SU ML: 0.055 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.088 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19963 1957 5 %RANDOM
Rwork0.16464 ---
all0.1663 37168 --
obs0.16638 37168 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.14 Å20 Å2
2--0.29 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 67 395 2540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222217
X-RAY DIFFRACTIONr_bond_other_d0.0030.021541
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9833010
X-RAY DIFFRACTIONr_angle_other_deg0.83233738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3935254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10523.509114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50415394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2111518
X-RAY DIFFRACTIONr_chiral_restr0.0890.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212346
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02468
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0021.51254
X-RAY DIFFRACTIONr_mcbond_other0.2491.5486
X-RAY DIFFRACTIONr_mcangle_it1.82322065
X-RAY DIFFRACTIONr_scbond_it2.7453963
X-RAY DIFFRACTIONr_scangle_it4.5584.5939
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 145 -
Rwork0.24 2758 -
obs--100 %

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