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- PDB-1ocu: Crystal structure of the yeast PX-domain protein Grd19p (sorting ... -

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Basic information

Entry
Database: PDB / ID: 1ocu
TitleCrystal structure of the yeast PX-domain protein Grd19p (sorting nexin 3) complexed to phosphatidylinosytol-3-phosphate.
ComponentsSORTING NEXIN
KeywordsSORTING PROTEIN / YEAST PROTEIN / SORTING NEXIN / COMPLEX WITH PHOSPHATIDYLINOSITOL PHOSPHATE
Function / homology
Function and homology information


WNT ligand biogenesis and trafficking / protein-lipid complex / late endosome to Golgi transport / retromer complex / phosphatidylinositol-3-phosphate binding / endocytic recycling / fungal-type vacuole membrane / protein localization / protein transport / early endosome membrane ...WNT ligand biogenesis and trafficking / protein-lipid complex / late endosome to Golgi transport / retromer complex / phosphatidylinositol-3-phosphate binding / endocytic recycling / fungal-type vacuole membrane / protein localization / protein transport / early endosome membrane / endosome / Golgi membrane / cytosol
Similarity search - Function
Fungal SNX3, PX domain / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PIB / Sorting nexin-3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhou, C.Z. / Li de La Sierra-Gallay, I. / Cheruel, S. / Collinet, B. / Minard, P. / Blondeau, K. / Henkes, G. / Aufrere, R. / Leulliot, N. / Graille, M. ...Zhou, C.Z. / Li de La Sierra-Gallay, I. / Cheruel, S. / Collinet, B. / Minard, P. / Blondeau, K. / Henkes, G. / Aufrere, R. / Leulliot, N. / Graille, M. / Sorel, I. / Savarin, P. / de la Torre, F. / Poupon, A. / Janin, J. / van Tilbeurgh, H.
CitationJournal: J. Biol. Chem. / Year: 2003
Title: Crystal structure of the yeast Phox homology (PX) domain protein Grd19p complexed to phosphatidylinositol-3-phosphate.
Authors: Zhou, C.Z. / Li de La Sierra-Gallay, I. / Quevillon-Cheruel, S. / Collinet, B. / Minard, P. / Blondeau, K. / Henckes, G. / Aufrere, R. / Leulliot, N. / Graille, M. / Sorel, I. / Savarin, P. ...Authors: Zhou, C.Z. / Li de La Sierra-Gallay, I. / Quevillon-Cheruel, S. / Collinet, B. / Minard, P. / Blondeau, K. / Henckes, G. / Aufrere, R. / Leulliot, N. / Graille, M. / Sorel, I. / Savarin, P. / de la Torre, F. / Poupon, A. / Janin, J. / van Tilbeurgh, H.
History
DepositionFeb 10, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity_src_gen / struct
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct.title
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SORTING NEXIN
B: SORTING NEXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8624
Polymers37,7542
Non-polymers1,1092
Water1,40578
1
A: SORTING NEXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4312
Polymers18,8771
Non-polymers5541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SORTING NEXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4312
Polymers18,8771
Non-polymers5541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)31.430, 55.760, 64.750
Angle α, β, γ (deg.)110.75, 97.35, 99.49
Int Tables number1
Space group name H-MP1

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Components

#1: Protein SORTING NEXIN /


Mass: 18876.814 Da / Num. of mol.: 2 / Fragment: PX-DOMAIN
Source method: isolated from a genetically manipulated source
Details: CHEMICALLY MODIFIED CYSTEINE. D-MYO-PHOSPHATIDYLINOSITOL 3-PHOSPHATE
Source: (gene. exp.) Saccharomyces cerevisiae S288C / Description: CLONED GENE / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08826
#2: Chemical ChemComp-PIB / 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE / D-MYO-PHOSPHATIDYLINOSITOL 3-PHOSPHATED (+)-SN-1,2-DI-O-BUTANOYLGLYCERYL,3-O-PHOSPHO


Mass: 554.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H32O16P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.72 Å3/Da / Density % sol: 54 %
Crystal growpH: 6.8
Details: 10% PEG8000, 8% ETHYLENE GLYCOL, 0.1M NA-HEPES PH 7,5
Crystal grow
*PLUS
Temperature: 293 K / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
17 mg/mlprotein1drop
22 mMdiC4PtdIns(3)P1drop
30.1 M1dropNaCl
410 mMbeta-mercaptoethanol1reservoir
520 mMTris-HCl1reservoirpH7
610 %PEG80001reservoir
78 %ethlene glycol1reservoir
80.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.984
DetectorDate: Jul 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.28→25 Å / Num. obs: 17289 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 25.1
Reflection shellResolution: 2.28→2.33 Å / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 3.2 / % possible all: 77.3
Reflection
*PLUS
Highest resolution: 2.28 Å / Lowest resolution: 25.08 Å / Num. all: 65105 / Num. obs: 11970 / % possible obs: 95.97 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 77.31 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OCS

1ocs


Resolution: 2.3→20 Å / Data cutoff high absF: 1000 / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 1 A TO 27 A AND 162 A, 1B TO 30 B ARE ABSENT FROM THE FINAL MODEL BECAUSE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1699 9.6 %RANDOM
Rwork0.221 ---
obs0.221 17072 96.8 %-
Displacement parametersBiso mean: 41.2 Å2
Baniso -1Baniso -2Baniso -3
1--15.893 Å2-1.446 Å27.882 Å2
2--9.085 Å2-0.079 Å2
3---6.808 Å2
Refine analyze
ObsFree
Luzzati coordinate error0.29 Å-
Luzzati d res low20 Å-
Luzzati sigma a-0.35 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2197 0 44 78 2319
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.32 Å / Total num. of bins used: 33 /
RfactorNum. reflection
Rfree0.2562 44
Rwork0.2758 392
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PIB.PARMAPIB.TOP
X-RAY DIFFRACTION3CME.PARAMCME.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
% reflection Rfree: 4.8 % / Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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