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- PDB-1upq: Crystal structure of the pleckstrin homology (PH) domain of PEPP1 -

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Basic information

Entry
Database: PDB / ID: 1upq
TitleCrystal structure of the pleckstrin homology (PH) domain of PEPP1
ComponentsPEPP1
KeywordsSIGNAL TRANSDUCTION / PH DOMAIN / PHOSPHOINOSITIDE BINDING
Function / homology
Function and homology information


positive regulation of Wnt signaling pathway, planar cell polarity pathway / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,5-bisphosphate binding / Synthesis of PIPs at the plasma membrane / extrinsic component of cytoplasmic side of plasma membrane / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of canonical Wnt signaling pathway / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
PKHA4-7, PH domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Pleckstrin homology domain-containing family A member 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsMilburn, C.C. / Komander, D. / Deak, M. / Alessi, D.R. / van Aalten, D.M.F.
CitationJournal: To be Published
Title: Crystal Structure of the Pleckstrin Homology Domain of Pepp1
Authors: Milburn, C.C. / Komander, D. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F.
History
DepositionOct 9, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Source and taxonomy / Structure summary / Category: audit_author / entity_src_gen
Item: _audit_author.name / _entity_src_gen.pdbx_host_org_cell_line ..._audit_author.name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4304
Polymers14,1421
Non-polymers2883
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.547, 93.547, 28.786
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-2034-

HOH

21A-2037-

HOH

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Components

#1: Protein PEPP1


Mass: 14142.014 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 45-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX4-T1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9H4M7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.17 Å3/Da / Density % sol: 43 %
Crystal growpH: 6.5
Details: 25% PEG 5000 MME, 0.2 M AMMONIUM SULFATE, 0.1 M MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.976262
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976262 Å / Relative weight: 1
ReflectionResolution: 1.48→27.5 Å / Num. obs: 20221 / % possible obs: 91.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.9 / % possible all: 97.5

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EAZ

1eaz


Resolution: 1.48→30 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Details: INITIALLY REFINED USING CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 511 5 %RANDOM
obs0.1809 -91.7 %-
all-101996 --
Refinement stepCycle: LAST / Resolution: 1.48→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms859 0 15 127 1001
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.016
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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