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- PDB-6ee0: Crystal Structure of SNX23 PX domain -

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Basic information

Entry
Database: PDB / ID: 6ee0
TitleCrystal Structure of SNX23 PX domain
ComponentsKinesin-like protein KIF16B
KeywordsLIPID BINDING PROTEIN / PX domain / endosome / trafficking / sorting nexin
Function / homology
Function and homology information


formation of primary germ layer / Golgi to endosome transport / receptor catabolic process / endoderm development / early endosome to late endosome transport / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,4-bisphosphate binding / Kinesins / plus-end-directed microtubule motor activity / phosphatidylinositol-3,5-bisphosphate binding ...formation of primary germ layer / Golgi to endosome transport / receptor catabolic process / endoderm development / early endosome to late endosome transport / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,4-bisphosphate binding / Kinesins / plus-end-directed microtubule motor activity / phosphatidylinositol-3,5-bisphosphate binding / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule-based movement / phosphatidylinositol-3,4,5-trisphosphate binding / regulation of receptor recycling / fibroblast growth factor receptor signaling pathway / epidermal growth factor receptor signaling pathway / spindle / microtubule binding / early endosome membrane / microtubule / early endosome / endosome / ATP hydrolysis activity / ATP binding / cytosol / cytoplasm
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 / FHA domain / Forkhead-associated (FHA) domain / Kinesin motor domain signature. ...Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / FHA domain / Forkhead-associated (FHA) domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / SMAD/FHA domain superfamily / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Kinesin-like protein KIF16B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.518 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 12, 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

Downloads & links

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Assembly

Deposited unit
A: Kinesin-like protein KIF16B
B: Kinesin-like protein KIF16B
C: Kinesin-like protein KIF16B


Theoretical massNumber of molelcules
Total (without water)46,8633
Polymers46,8633
Non-polymers00
Water34219
1
A: Kinesin-like protein KIF16B


Theoretical massNumber of molelcules
Total (without water)15,6211
Polymers15,6211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kinesin-like protein KIF16B


Theoretical massNumber of molelcules
Total (without water)15,6211
Polymers15,6211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Kinesin-like protein KIF16B


Theoretical massNumber of molelcules
Total (without water)15,6211
Polymers15,6211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.783, 92.836, 47.039
Angle α, β, γ (deg.)90.00, 91.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kinesin-like protein KIF16B / Sorting nexin-23


Mass: 15621.159 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF16B, C20orf23, KIAA1590, SNX23 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96L93
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 50 mM Tris (pH 8.5), 0.2 M NaCl, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.518→47.03 Å / Num. obs: 13562 / % possible obs: 99 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.039 / Net I/σ(I): 8.8
Reflection shellResolution: 2.518→2.62 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1488 / CC1/2: 0.706 / Rpim(I) all: 0.428 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V14

2v14


Resolution: 2.518→47.027 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 1286 10.04 %
Rwork0.178 --
obs0.1848 12806 93.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.518→47.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3292 0 0 19 3311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013379
X-RAY DIFFRACTIONf_angle_d1.3484541
X-RAY DIFFRACTIONf_dihedral_angle_d13.141276
X-RAY DIFFRACTIONf_chiral_restr0.056486
X-RAY DIFFRACTIONf_plane_restr0.006568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5181-2.61890.36221360.27851101X-RAY DIFFRACTION82
2.6189-2.73810.34661320.26211177X-RAY DIFFRACTION86
2.7381-2.88240.391370.25841228X-RAY DIFFRACTION91
2.8824-3.0630.33351480.25261267X-RAY DIFFRACTION93
3.063-3.29940.31451420.23331322X-RAY DIFFRACTION97
3.2994-3.63140.25891430.19441349X-RAY DIFFRACTION98
3.6314-4.15650.2541540.16751337X-RAY DIFFRACTION98
4.1565-5.23570.18281470.14241361X-RAY DIFFRACTION98
5.2357-47.03530.19831470.14131378X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.46983.00460.95547.7695-1.36875.6501-0.11520.32560.4611-0.15310.00380.5392-0.2813-0.57690.20750.33270.03690.03670.4820.06120.4947-37.303419.44266.4889
29.49530.72522.99192.1205-1.84673.2814-0.2434-0.86391.41941.6158-0.01850.72581.6104-1.29590.77311.067-0.04720.01730.75740.01370.8662-39.546915.76381.185
35.38973.16312.22364.96182.59564.0985-0.05960.3231-0.31290.2542-0.2103-0.00561.5812-0.52450.09040.73730.00660.0230.49360.08360.5877-34.045211.958367.6026
47.96330.6718-0.01952.81991.58157.831-0.09871.86320.6181-1.435-0.02250.5517-0.61610.31960.07940.7233-0.0676-0.08020.92380.20580.5771-36.627618.755354.6226
59.263-1.3085-0.84568.1007-0.18947.54340.1298-0.34570.00620.60560.0777-0.00040.21030.1886-0.21920.4941-0.0712-0.01250.44520.03580.3455-19.232419.898586.4182
66.7957-5.91023.54896.91860.57486.9686-1.0075-0.53431.54941.69421.0508-2.00510.07440.83120.01890.6263-0.1078-0.1910.7872-0.07760.8984-9.296526.417491.2777
76.1143-6.0121-0.35369.1224-0.56922.4632-0.2906-0.2044-0.14180.15640.1833-0.21680.2889-0.01030.14010.4433-0.0846-0.03970.44620.020.3135-13.060214.148485.6096
85.1754-2.73641.51966.4221.53626.5226-0.01730.18490.0487-0.7124-0.0389-0.30930.21120.6-0.08380.3370.0092-0.0120.3927-0.07340.4372-30.6149-9.997969.8706
98.0401-4.4879-3.42267.74664.21935.6968-0.0138-0.65670.6477-0.02550.2988-0.4139-0.20160.1504-0.35070.64430.016-0.06510.41920.02220.4997-35.4336-3.004878.2669
108.6292-3.6972-4.58292.87083.00563.2267-0.2615-0.89091.8805-0.25880.6755-1.20430.04810.9035-0.62640.9083-0.0514-0.03760.5835-0.05331.1984-18.3837-4.524478.348
114.2284-4.815-3.98635.1984.85876.9716-0.4863-1.2810.45560.33220.8839-0.43070.39190.8005-0.46670.44230.0812-0.05570.4191-0.06450.5358-32.0193-9.584382.1896
124.29220.24310.0122.65-0.58643.25870.7517-2.30480.42731.2607-0.85230.03520.6246-3.2995-0.45720.798-0.1379-0.1111.3823-0.05950.7731-51.8778-9.842885.451
136.9721-2.4032-4.38065.85122.20347.14670.05980.4936-0.5251-0.6916-0.14770.6072-0.7147-1.1795-0.10690.63550.0447-0.17930.63330.01560.5248-42.3263-4.930770.8457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1181 through 1240 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1241 through 1253 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1254 through 1284 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1285 through 1312 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1181 through 1232 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1233 through 1253 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1254 through 1312 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1181 through 1210 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1211 through 1240 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1241 through 1253 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1254 through 1284 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1285 through 1293 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1294 through 1312 )

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