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- PDB-7wf6: Crystal structure of SNX13 RGS domain -

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Basic information

Entry
Database: PDB / ID: 7wf6
TitleCrystal structure of SNX13 RGS domain
ComponentsSorting nexin-13
KeywordsPROTEIN TRANSPORT / Sorting nexin / RGS
Function / homology
Function and homology information


phosphatidylinositol-3-phosphate binding / negative regulation of signal transduction / phosphatidylinositol binding / intracellular protein transport / positive regulation of GTPase activity / early endosome membrane / early endosome / intracellular membrane-bounded organelle
Similarity search - Function
Sorting nexin-13, PX domain / SNX13, RGS domain / Phox-associated domain / Sorting nexin, C-terminal / PXA domain / Sorting nexin C terminal / PXA domain profile. / Domain associated with PX domains / PhoX homologous domain, present in p47phox and p40phox. / Regulator of G protein signaling domain ...Sorting nexin-13, PX domain / SNX13, RGS domain / Phox-associated domain / Sorting nexin, C-terminal / PXA domain / Sorting nexin C terminal / PXA domain profile. / Domain associated with PX domains / PhoX homologous domain, present in p47phox and p40phox. / Regulator of G protein signaling domain / PX domain profile. / RGS, subdomain 2 / PX domain / Phox homology / PX domain superfamily / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsXu, J. / Zhu, J. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171213 China
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Structural Studies Reveal Unique Non-canonical Regulators of G Protein Signaling Homology (RH) Domains in Sorting Nexins.
Authors: Zhang, Y. / Chen, R. / Dong, Y. / Zhu, J. / Su, K. / Liu, J. / Xu, J.
History
DepositionDec 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sorting nexin-13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0435
Polymers17,9011
Non-polymers1424
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint-30 kcal/mol
Surface area8960 Å2
Unit cell
Length a, b, c (Å)165.328, 165.328, 165.328
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein Sorting nexin-13 / / RGS domain- and PHOX domain-containing protein / RGS-PX1


Mass: 17901.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX13, KIAA0713 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y5W8
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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

CrystalMosaicity: 0 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5 / Details: 0.7 M Sodium citrate tribasic, 0.1 M TRIS pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.25→29.23 Å / Num. obs: 12744 / % possible obs: 99.9 % / Redundancy: 40.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.383 / Rpim(I) all: 0.061 / Rrim(I) all: 0.389 / Net I/σ(I): 9.2 / Num. measured all: 516745 / Scaling rejects: 8767
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.25-3.5139.91.14210127025380.6090.1821.1574100
8.59-29.2328.90.232225297800.9880.0410.23514.497.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C7K

3c7k


Resolution: 3.25→18 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.94 / SU B: 11.973 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 621 4.9 %RANDOM
Rwork0.2185 ---
obs0.2188 11986 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 200 Å2 / Biso mean: 98.134 Å2 / Biso min: 66.49 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 3.25→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 4 0 1203
Biso mean--105.28 --
Num. residues----145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131224
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171115
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.6471656
X-RAY DIFFRACTIONr_angle_other_deg1.2881.5722577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1225143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42822.17978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.30315213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2411510
X-RAY DIFFRACTIONr_chiral_restr0.0720.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021367
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02271
LS refinement shellResolution: 3.25→3.332 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 38 -
Rwork0.415 853 -
all-891 -
obs--100 %

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