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- PDB-1fao: STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN FROM DAPP1/PHISH IN C... -

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Basic information

Entry
Database: PDB / ID: 1fao
TitleSTRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN FROM DAPP1/PHISH IN COMPLEX WITH INOSITOL 1,3,4,5-TETRAKISPHOSPHATE
ComponentsDUAL ADAPTOR OF PHOSPHOTYROSINE AND 3-PHOSPHOINOSITIDES
KeywordsSIGNALING PROTEIN / PLECKSTRIN / 3-PHOSPHOINOSITIDES / INOSITOL TETRAKISPHOSPHATE SIGNAL TRANSDUCTION PROTEIN / ADAPTOR PROTEIN
Function / homology
Function and homology information


phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,4,5-trisphosphate binding / protein dephosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / phospholipid binding / signal transduction / plasma membrane / cytosol
Similarity search - Function
DAPP1, SH2 domain / : / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH2 domain / Src homology 2 (SH2) domain profile. ...DAPP1, SH2 domain / : / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE / Dual adapter for phosphotyrosine and 3-phosphotyrosine and 3-phosphoinositide
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFerguson, K.M. / Kavran, J.M. / Sankaran, V.G. / Fournier, E. / Isakoff, S.J. / Skolnik, E.Y. / Lemmon, M.A.
CitationJournal: 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 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUAL ADAPTOR OF PHOSPHOTYROSINE AND 3-PHOSPHOINOSITIDES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3052
Polymers14,8051
Non-polymers5001
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.674, 46.273, 64.743
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

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Components

#1: Protein DUAL ADAPTOR OF PHOSPHOTYROSINE AND 3-PHOSPHOINOSITIDES / DAPP1 / PHISH / BAM32


Mass: 14805.023 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH INOSITOL 1,3,4,5-TETRAKISPHOSPHATE / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UN19
#2: Chemical ChemComp-4IP / INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE


Mass: 500.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16O18P4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3450, Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112.5 %PEG345011
250 mMTris11
325 mMsodium phosphate12
425 mg/mlprotein12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Feb 10, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 11260 / Num. obs: 11260 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 26.6
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 29 / Num. unique all: 966 / Rsym value: 0.05 / % possible all: 99.4
Reflection
*PLUS
Num. measured all: 50768
Reflection shell
*PLUS
% possible obs: 99.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1FB8: UNLIGANDED DAPP1

1fb8


Resolution: 1.8→30 Å / Rfactor Rfree error: 0.007 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1083 9.5 %RANDOM
Rwork0.219 ---
all-11421 --
obs-11421 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.12 Å2 / ksol: 0.398 e/Å3
Displacement parametersBiso mean: 16.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å20 Å20 Å2
2---2.97 Å20 Å2
3---0.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms838 0 28 105 971
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.621.5
X-RAY DIFFRACTIONc_mcangle_it2.012
X-RAY DIFFRACTIONc_scbond_it2.722
X-RAY DIFFRACTIONc_scangle_it3.452.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.277 201 10.5 %
Rwork0.226 1722 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4PARAM.IP4TOP.IP4
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 9.5 % / Rfactor obs: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.277 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.226

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