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- PDB-4bgj: Crystal structure of the phox-homology domain of human sorting ne... -

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Basic information

Entry
Database: PDB / ID: 4bgj
TitleCrystal structure of the phox-homology domain of human sorting nexin 14
ComponentsSORTING NEXIN-14
KeywordsPROTEIN TRANSPORT
Function / homology
Function and homology information


phosphatidylinositol-3,5-bisphosphate binding / postsynaptic modulation of chemical synaptic transmission / autophagosome maturation / phosphatidylinositol binding / protein transport / late endosome / late endosome membrane / postsynapse / lysosome / lysosomal membrane ...phosphatidylinositol-3,5-bisphosphate binding / postsynaptic modulation of chemical synaptic transmission / autophagosome maturation / phosphatidylinositol binding / protein transport / late endosome / late endosome membrane / postsynapse / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / dendrite / cytosol
Similarity search - Function
Sorting nexin-14, PX domain / SNX14, RGS 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 ...Sorting nexin-14, PX domain / SNX14, RGS 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. / Regulator of G protein signaling domain / RGS, subdomain 2 / PX domain profile. / PX domain / Phox homology / PX domain superfamily / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsVollmar, M. / Kiyani, W. / Shrestha, L. / Goubin, S. / Krojer, T. / Pike, A.C.W. / Carpenter, E. / Quigley, A. / McKenzie, A. / Burgess-Brown, N. ...Vollmar, M. / Kiyani, W. / Shrestha, L. / Goubin, S. / Krojer, T. / Pike, A.C.W. / Carpenter, E. / Quigley, A. / McKenzie, A. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Yue, W.W.
CitationJournal: To be Published
Title: Crystal Structure of the Phox-Homology Domain of Human Sorting Nexin 14
Authors: Vollmar, M. / Kiyani, W. / Shrestha, L. / Goubin, S. / Krojer, T. / Pike, A.C.W. / Carpenter, E. / Quigley, A. / Mckenzie, A. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / ...Authors: Vollmar, M. / Kiyani, W. / Shrestha, L. / Goubin, S. / Krojer, T. / Pike, A.C.W. / Carpenter, E. / Quigley, A. / Mckenzie, A. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Yue, W.W.
History
DepositionMar 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SORTING NEXIN-14


Theoretical massNumber of molelcules
Total (without water)17,3991
Polymers17,3991
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.611, 88.611, 73.082
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein SORTING NEXIN-14 /


Mass: 17398.682 Da / Num. of mol.: 1 / Fragment: PHOX-HOMOLOGY DOMAIN, RESIDUES 505-649
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RARE / References: UniProt: Q9Y5W7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 4.12 Å3/Da / Density % sol: 70.16 % / Description: NONE
Crystal growDetails: 20%(W/V) PEG 3350, 0.2M SODIUM MALONATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0163
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0163 Å / Relative weight: 1
ReflectionResolution: 2.44→23.49 Å / Num. obs: 9277 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.4
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XTN

1xtn


Resolution: 2.55→23.49 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.948 / SU B: 15.975 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. UNEXPLAINED DIFFERENCE ELECTRON DENSITY AT SER623
RfactorNum. reflection% reflectionSelection details
Rfree0.22566 443 4.8 %RANDOM
Rwork0.20523 ---
obs0.20625 8839 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.969 Å2
Baniso -1Baniso -2Baniso -3
1--2.44 Å20 Å20 Å2
2---2.44 Å20 Å2
3---4.88 Å2
Refinement stepCycle: LAST / Resolution: 2.55→23.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 0 4 960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.019983
X-RAY DIFFRACTIONr_bond_other_d0.0010.02884
X-RAY DIFFRACTIONr_angle_refined_deg0.9661.9541331
X-RAY DIFFRACTIONr_angle_other_deg0.68532024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7395114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.19423.33351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94515150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.102157
X-RAY DIFFRACTIONr_chiral_restr0.0590.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211106
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02247
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_it5.3311.356468
X-RAY DIFFRACTIONr_mcbond_other5.32811.344467
X-RAY DIFFRACTIONr_mcangle_it7.7121.162578
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.05811.517515
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.551→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 33 -
Rwork0.402 650 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 11.7935 Å / Origin y: -7.1252 Å / Origin z: -11.539 Å
111213212223313233
T0.122 Å20.0252 Å2-0.0157 Å2-0.0998 Å20.0151 Å2--0.1016 Å2
L4.141 °2-0.094 °2-1.518 °2-2.3481 °2-0.1289 °2--1.8958 °2
S0.0897 Å °-0.0985 Å °0.0595 Å °-0.3752 Å °0.0567 Å °-0.0761 Å °-0.0919 Å °-0.1371 Å °-0.1464 Å °

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