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- PDB-1fb8: STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN FROM DAPP1/PHISH -

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Basic information

Entry
Database: PDB / ID: 1fb8
TitleSTRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN FROM DAPP1/PHISH
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
PHOSPHATE ION / Dual adapter for phosphotyrosine and 3-phosphotyrosine and 3-phosphoinositide
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 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 14, 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: Derived calculations / Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
A: DUAL ADAPTOR OF PHOSPHOTYROSINE AND 3-PHOSPHOINOSITIDES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9953
Polymers14,8051
Non-polymers1902
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DUAL ADAPTOR OF PHOSPHOTYROSINE AND 3-PHOSPHOINOSITIDES
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)59,98012
Polymers59,2204
Non-polymers7608
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area6780 Å2
ΔGint-84 kcal/mol
Surface area23670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)83.380, 83.380, 38.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
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
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UN19
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.26 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3450, Ethylene Glycol, Ammonium Phosphate, Sodium Phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 %PEG34501reservoir
220-30 %ethylene glycol1reservoir
350 mM1reservoirNaPO4
4200 mMammonium phosphate1reservoir
525 mMsodium phosphate1drop
625 mg/mlprotein1drop

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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: 2.4→50 Å / Num. all: 4973 / Num. obs: 4973 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.04 / Net I/σ(I): 21.5
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 5.2 / Num. unique all: 717 / Rsym value: 0.14 / % possible all: 84
Reflection
*PLUS
Num. measured all: 17635
Reflection shell
*PLUS
% possible obs: 81.3 % / Mean I/σ(I) obs: 5.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS0.9refinement
RefinementMethod to determine structure: MIR / Resolution: 2.4→35 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 708822.74 / 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
Rfree0.272 740 14.9 %RANDOM
Rwork0.223 ---
obs0.223 4973 93.9 %-
all-4973 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.75 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso mean: 43.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.4→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms879 0 10 28 917
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it2.281.5
X-RAY DIFFRACTIONc_mcangle_it3.442
X-RAY DIFFRACTIONc_scbond_it3.862
X-RAY DIFFRACTIONc_scangle_it5.012.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 102 14.2 %
Rwork0.271 615 -
obs--84 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4
X-RAY DIFFRACTION5
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 35 Å / σ(F): 0 / % reflection Rfree: 14.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 43.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68
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: 0.321 / % reflection Rfree: 14.2 % / Rfactor Rwork: 0.271

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