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- PDB-3hpb: Crystal structure of SNX5-PX domain in P212121 space group -

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Basic information

Entry
Database: PDB / ID: 3hpb
TitleCrystal structure of SNX5-PX domain in P212121 space group
ComponentsSnx5 protein
KeywordsPROTEIN TRANSPORT / Sorting nexin / SNX5 / Phox / PhosphatidylInositol / PI(4 / 5)P2
Function / homology
Function and homology information


epidermal growth factor catabolic process / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / Golgi Associated Vesicle Biogenesis / phosphatidylinositol-5-phosphate binding / retromer complex / retrograde transport, endosome to Golgi / phosphatidylinositol-4-phosphate binding ...epidermal growth factor catabolic process / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / Golgi Associated Vesicle Biogenesis / phosphatidylinositol-5-phosphate binding / retromer complex / retrograde transport, endosome to Golgi / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / dynactin binding / phagocytic cup / brush border / D1 dopamine receptor binding / positive regulation of insulin receptor signaling pathway / ruffle / negative regulation of blood pressure / phosphatidylinositol binding / intracellular protein transport / cytoplasmic side of plasma membrane / endosome / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / cytosol
Similarity search - Function
SNX5, PX domain / Sorting nexin-5 / Sorting nexin-5/6/32 / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Phox-like domain / PX Domain / PX domain profile. / PX domain / Phox homology ...SNX5, PX domain / Sorting nexin-5 / Sorting nexin-5/6/32 / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Phox-like domain / PX Domain / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.19 Å
AuthorsKoharudin, L.M.I. / Furey, W. / Gronenborn, A.M.
CitationJournal: To be Published
Title: The Phox domain of sorting nexin 5 lacks ptdins(3)p specificity and preferentially binds to ptdins(4,5)P2
Authors: Koharudin, L.M.I. / Furey, W. / Liu, H. / Liu, Y.-J. / Gronenborn, A.M.
History
DepositionJun 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Snx5 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6852
Polymers18,6501
Non-polymers351
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.957, 75.874, 77.512
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Snx5 protein /


Mass: 18649.512 Da / Num. of mol.: 1 / Fragment: Residues 20-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snx5 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1H267
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE ORIGINAL CONSTRUCT CONTAINED RESIDUES 1-180. THE FINAL CRYSTALLIZED PROTEIN CONSTRUCT SPANS ...THE ORIGINAL CONSTRUCT CONTAINED RESIDUES 1-180. THE FINAL CRYSTALLIZED PROTEIN CONSTRUCT SPANS FROM RESIDUES 20 TO 180 DUE TO NON-SPECIFIC CLEAVAGE BY THROMBIN PROTEASE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 277 K / pH: 8
Details: the protein solution in the final superdex-75 buffer (20 mM Tris.HCl, 100 mM NaCl, 0.02% NaN3, pH 8.0) was concentrated to 8 mg/ml. The Se-Met derivative and the 2.19 A crystals were ...Details: the protein solution in the final superdex-75 buffer (20 mM Tris.HCl, 100 mM NaCl, 0.02% NaN3, pH 8.0) was concentrated to 8 mg/ml. The Se-Met derivative and the 2.19 A crystals were obtained using an optimized initial crystallization condition of 8 ul of protein vs 1 ul of reservoir solution (0.2M (NH4)2SO4, 0.1M Sodium cacodylate tryhydrate pH 6.5, 30% PEG 8000) at 4C by sitting drop vapor diffusion, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelengthWavelength (Å)
ROTATING ANODERIGAKU FR-E SUPERBRIGHT11.5418
SYNCHROTRONAPS 22-ID20.9793,0.9795,0.9718
Detector
TypeIDDetectorDateDetails
RIGAKU SATURN 9441CCDOct 17, 2006MIRRORS
MARMOSAIC 300 mm CCD2CCDNov 18, 2008ROSENBAUM-ROCK MONOCHROMATOR HIGH-RESOLUTION DOUBLE-CRYSTAL SI(220) SAGITTAL FO CUSING, ROSENBAUM- ROCK VERTICAL FOCUSING MIRROR
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1OSMIC MIRRORSSINGLE WAVELENGTHMx-ray1
2SI 220. ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATORMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97931
30.97951
40.97181
ReflectionResolution: 2.19→28.78 Å / Num. obs: 12680 / % possible obs: 93.4 % / Observed criterion σ(I): 3 / Redundancy: 4.18 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 28.1
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 2.05 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 3.5 / % possible all: 62.3

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Processing

Software
NameVersionClassification
StructureStudiodata collection
SnBphasing
PHASERphasing
REFMAC5.5.0044refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.19→28.78 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.449 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1244 9.8 %RANDOM
Rwork0.236 ---
obs0.24 11436 93.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.12 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20 Å2
2--0.15 Å2-0 Å2
3---1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.19→28.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 1 135 1410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221309
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2841.9661783
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2595161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.29825.31364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21315229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.943155
X-RAY DIFFRACTIONr_chiral_restr0.1010.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211009
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6821.5799
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32421315
X-RAY DIFFRACTIONr_scbond_it2.1563510
X-RAY DIFFRACTIONr_scangle_it3.6634.5468
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.47 68 -
Rwork0.322 497 -
obs--57.01 %

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