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- PDB-3hpc: Crystal structure of SNX5-PX domain in P21 space group -

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Basic information

Entry
Database: PDB / ID: 3hpc
TitleCrystal structure of SNX5-PX domain in P21 space group
ComponentsSnx5 protein
KeywordsPROTEIN TRANSPORT / Sprting nexin / SNX5 / Phox / SNX5-PX / PhosphatidylInositol / PI(4 / 5)P2 / CELL ADHESION
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 / MOLECULAR REPLACEMENT / Resolution: 1.47 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 1.2Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
X: Snx5 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5442
Polymers18,5091
Non-polymers351
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.598, 41.424, 47.227
Angle α, β, γ (deg.)90.00, 92.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Snx5 protein /


Mass: 18508.824 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.: 238 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.300956 Å3/Da / Density % sol: 46.543972 %
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 and crystallization were obtained using an optimized ...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 and crystallization were obtained using an optimized crystallization condition of 8ul of protein vs 1ul of reservoir solution (0.2M NH4CH3COO, 0.1M Sodium cacodylate tryhydrate pH 6.5, 30% PEG 4000), VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 15, 2007 / Details: MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.47→31.12 Å / Num. obs: 28322 / % possible obs: 98.3 % / Observed criterion σ(I): 3 / Redundancy: 4.13 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 20.1
Reflection shellResolution: 1.47→1.52 Å / Redundancy: 2.65 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 1.4 / % possible all: 90.8

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0044refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HPB
Resolution: 1.47→31.12 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.265 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1440 5.1 %RANDOM
Rwork0.184 ---
obs0.187 26873 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å2-0.01 Å2
2--0.61 Å2-0 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.47→31.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 1 238 1562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221362
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9641863
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7395173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.1325.38565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85615240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.311155
X-RAY DIFFRACTIONr_chiral_restr0.0970.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211061
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_it2.8271.5838
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.04721387
X-RAY DIFFRACTIONr_scbond_it5.5673524
X-RAY DIFFRACTIONr_scangle_it8.0364.5476
X-RAY DIFFRACTIONr_rigid_bond_restr3.33431362
X-RAY DIFFRACTIONr_sphericity_free14.9523252
X-RAY DIFFRACTIONr_sphericity_bonded11.58431323
LS refinement shellResolution: 1.47→1.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.45 103 -
Rwork0.421 1753 -
obs--88.17 %

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