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- PDB-1eaz: Crystal structure of the phosphoinositol (3,4)-bisphosphate bindi... -

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Basic information

Entry
Database: PDB / ID: 1eaz
TitleCrystal structure of the phosphoinositol (3,4)-bisphosphate binding PH domain of TAPP1 from human.
ComponentsTANDEM PH DOMAIN CONTAINING PROTEIN-1
KeywordsLIPID BINDING PROTEIN / LIPID-BINDING PROTEIN / LIPID DEGRADATION / PH DOMAIN / PHOSPHATIDYLINOSITOL (3 / 4)-BISPHOSPHATE / SIGNALLING
Function / homology
Function and homology information


luteinization / Leydig cell differentiation / ruffle organization / phosphatidylinositol-3,4-bisphosphate binding / estrogen metabolic process / face morphogenesis / skeletal system morphogenesis / platelet-derived growth factor receptor signaling pathway / Synthesis of PIPs at the plasma membrane / roof of mouth development ...luteinization / Leydig cell differentiation / ruffle organization / phosphatidylinositol-3,4-bisphosphate binding / estrogen metabolic process / face morphogenesis / skeletal system morphogenesis / platelet-derived growth factor receptor signaling pathway / Synthesis of PIPs at the plasma membrane / roof of mouth development / androgen metabolic process / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / post-embryonic development / B cell receptor signaling pathway / PDZ domain binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / establishment of protein localization / phospholipid binding / ruffle membrane / multicellular organism growth / cellular response to hydrogen peroxide / spermatogenesis / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / 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
CITRIC ACID / Pleckstrin homology domain-containing family A member 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsThomas, C.C. / Dowler, S. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F.
Citation
Journal: Biochem.J. / Year: 2001
Title: Crystal Structure of the Phosphatidylinositol 3,4-Bisphosphate-Binding Pleckstrin Homology (Ph) Domain of Tandem Ph-Domain-Containing Protein 1 (Tapp1): Molecular Basis of Lipid Specificity
Authors: Thomas, C.C. / Dowler, S. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F.
#1: Journal: Biochem.J. / Year: 2000
Title: Identification of Pleckstrin-Homology-Domain-Containing Proteins with Novel Phosphoinositide-Binding Specificities
Authors: Dowler, S. / Currie, R.A. / Campbell, D.G. / Deak, M. / Kular, G. / Downes, C.P. / Alessi, D.R.
#2: Journal: Mol.Cell / Year: 2000
Title: Structural Basis for Discrimination of 3-Phosphoinositides by Pleckstrin Homology Domains
Authors: Ferguson, K.M. / Kavran, J.M. / Sankaran, V.G. / Fournier, E. / Isakoff, S.J. / Skolnik, E.Y. / Lemmon, M.A.
History
DepositionJul 17, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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

Downloads & links

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Assembly

Deposited unit
A: TANDEM PH DOMAIN CONTAINING PROTEIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4322
Polymers14,2401
Non-polymers1921
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)65.017, 102.796, 41.471
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2107-

HOH

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Components

#1: Protein TANDEM PH DOMAIN CONTAINING PROTEIN-1 / TAPP1 N-TERMINAL PH DOMAIN


Mass: 14240.303 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN RESIDUES 182-303
Source method: isolated from a genetically manipulated source
Details: ORDERED CITRATE MOLECULE IN LIPID BINDING POCKET / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9HB21
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN IS PH DOMAIN FROM ACCESSION NUMBER PROTEIN

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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: 2.48 Å3/Da / Density % sol: 48 %
Crystal growpH: 5.6
Details: 0.085M SODIUM CITRATE, 25.5% PEG 4000, 15% GLYCEROL, 0.17M AMMONIUM ACETATE, pH 5.60
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114.5 mg/mlprotein1drop
20.085 Msodium citrate1reservoirpH5.6
325.5 %(w/v)PEG40001reservoir
415 %(v/v)glycerol1reservoir
50.17 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9999
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 25, 2001 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.4→27.524 Å / Num. obs: 27661 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.7
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 4.2 / % possible all: 97.7
Reflection
*PLUS
Lowest resolution: 30 Å
Reflection shell
*PLUS
% possible obs: 97.7 %

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FB8

1fb8


Resolution: 1.4→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: MODEL BUILT WITH WARPNTRACE, REFINEMENT STARTED USING CNS THEN USED SHELXL USED ANISOTROPIC B-FACTORS IN SHELXL REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1076 5 %RANDOM
obs0.171 -98.9 %-
all-27661 --
Refine analyzeOccupancy sum non hydrogen: 990
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms840 0 13 135 988
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d1.98
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
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.98

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