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- PDB-1btn: STRUCTURE OF THE BINDING SITE FOR INOSITOL PHOSPHATES IN A PH DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1btn
TitleSTRUCTURE OF THE BINDING SITE FOR INOSITOL PHOSPHATES IN A PH DOMAIN
ComponentsBETA-SPECTRIN
KeywordsSIGNAL TRANSDUCTION PROTEIN
Function / homology
Function and homology information


Interaction between L1 and Ankyrins / regulation of SMAD protein signal transduction / RHOV GTPase cycle / membrane assembly / RHOU GTPase cycle / central nervous system formation / NCAM signaling for neurite out-growth / cuticular plate / spectrin / COPI-mediated anterograde transport ...Interaction between L1 and Ankyrins / regulation of SMAD protein signal transduction / RHOV GTPase cycle / membrane assembly / RHOU GTPase cycle / central nervous system formation / NCAM signaling for neurite out-growth / cuticular plate / spectrin / COPI-mediated anterograde transport / RAF/MAP kinase cascade / plasma membrane organization / Golgi to plasma membrane protein transport / actin filament capping / M band / ankyrin binding / cortical actin cytoskeleton / cortical cytoskeleton / mitotic cytokinesis / axolemma / endomembrane system / regulation of protein localization to plasma membrane / positive regulation of interleukin-2 production / central nervous system development / cell projection / protein localization to plasma membrane / phospholipid binding / positive regulation of protein localization to plasma membrane / structural constituent of cytoskeleton / actin filament binding / GTPase binding / cell junction / actin cytoskeleton organization / postsynapse / postsynaptic density / calmodulin binding / glutamatergic synapse / protein-containing complex binding / nucleolus / protein-containing complex / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Pleckstrin homology domain, spectrin-type / Pleckstrin homology domain 9 / Pleckstrin homology domain / Spectrin, beta subunit / Spectrin repeat / Spectrin repeat / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Spectrin/alpha-actinin ...Pleckstrin homology domain, spectrin-type / Pleckstrin homology domain 9 / Pleckstrin homology domain / Spectrin, beta subunit / Spectrin repeat / Spectrin repeat / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Spectrin/alpha-actinin / Spectrin repeats / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Spectrin beta chain, non-erythrocytic 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsWilmanns, M. / Hyvoenen, M. / Saraste, M.
Citation
Journal: EMBO J. / Year: 1995
Title: Structure of the binding site for inositol phosphates in a PH domain.
Authors: Hyvonen, M. / Macias, M.J. / Nilges, M. / Oschkinat, H. / Saraste, M. / Wilmanns, M.
#1: Journal: Nature / Year: 1994
Title: Structure of the Ph Domain from Beta-Spectrin
Authors: Macias, M.J. / Musacchio, A. / Postingl, H. / Nilges, M. / Saraste, M. / Oschkinat, H.
History
DepositionAug 23, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: BETA-SPECTRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7082
Polymers12,2881
Non-polymers4201
Water1,38777
1
A: BETA-SPECTRIN
hetero molecules

A: BETA-SPECTRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4164
Polymers24,5762
Non-polymers8402
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Unit cell
Length a, b, c (Å)69.000, 69.000, 50.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein BETA-SPECTRIN


Mass: 12287.853 Da / Num. of mol.: 1 / Fragment: PH DOMAIN, RESIDUES 2199 - 2304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: MUSSPNA.GBROD / Organ: BRAIN / Plasmid: PET21D / Species (production host): Escherichia coli / Gene (production host): MUSSPNA.GBROD / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q62261
#2: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol trisphosphate


Mass: 420.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O15P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
210 mMsodium phosphate1drop
410-15 %(w/v)PEG60001reservoir
530 %(v/v)ethanol1reservoir
6100 mMsodium acetate1reservoir
3Ins(1,4,5)P31drop3-fold excess

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→1000 Å / Num. obs: 7830 / % possible obs: 89.6 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.047
Reflection
*PLUS
Num. measured all: 41713 / Rmerge(I) obs: 0.047

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2→8 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.286 --
Rwork0.205 --
obs0.205 7573 88.6 %
Displacement parametersBiso mean: 27.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms864 0 24 77 965
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.501
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.62
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.346
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.62
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.346

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