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- PDB-1zm0: Crystal Structure of the Carboxyl Terminal PH Domain of Pleckstri... -

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Basic information

Entry
Database: PDB / ID: 1zm0
TitleCrystal Structure of the Carboxyl Terminal PH Domain of Pleckstrin To 2.1 Angstroms
ComponentsPleckstrin
KeywordsLIPID BINDING PROTEIN / PH DOMAIN / BETA SANDWICH / PLECKSTRIN
Function / homology
Function and homology information


positive regulation of inositol-polyphosphate 5-phosphatase activity / protein secretion by platelet / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / regulation of cell diameter / thrombin-activated receptor signaling pathway / negative regulation of inositol phosphate biosynthetic process / negative regulation of calcium-mediated signaling / positive regulation of actin filament depolymerization / protein kinase C signaling / platelet degranulation ...positive regulation of inositol-polyphosphate 5-phosphatase activity / protein secretion by platelet / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / regulation of cell diameter / thrombin-activated receptor signaling pathway / negative regulation of inositol phosphate biosynthetic process / negative regulation of calcium-mediated signaling / positive regulation of actin filament depolymerization / protein kinase C signaling / platelet degranulation / negative regulation of G protein-coupled receptor signaling pathway / phosphatidylinositol metabolic process / positive regulation of integrin activation / positive regulation of actin filament bundle assembly / cell projection organization / ruffle organization / phosphatidylinositol-3,4-bisphosphate binding / positive regulation of platelet activation / vesicle docking involved in exocytosis / cortical actin cytoskeleton organization / hematopoietic progenitor cell differentiation / integrin-mediated signaling pathway / protein kinase C binding / platelet aggregation / ruffle membrane / Platelet degranulation / actin cytoskeleton organization / protein homodimerization activity / extracellular region / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Pleckstrin, DEP domain / : / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. ...Pleckstrin, DEP domain / : / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP 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 / Winged helix DNA-binding domain superfamily / Roll / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJackson, S.G. / Zhang, Y. / Zhang, K. / Summerfield, R. / Haslam, R.J. / Junop, M.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of the carboxy-terminal PH domain of pleckstrin at 2.1 Angstroms.
Authors: Jackson, S.G. / Zhang, Y. / Bao, X. / Zhang, K. / Summerfield, R. / Haslam, R.J. / Junop, M.S.
History
DepositionMay 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pleckstrin
B: Pleckstrin


Theoretical massNumber of molelcules
Total (without water)26,0422
Polymers26,0422
Non-polymers00
Water2,936163
1
A: Pleckstrin


Theoretical massNumber of molelcules
Total (without water)13,0211
Polymers13,0211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pleckstrin


Theoretical massNumber of molelcules
Total (without water)13,0211
Polymers13,0211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Pleckstrin

A: Pleckstrin


Theoretical massNumber of molelcules
Total (without water)26,0422
Polymers26,0422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area1830 Å2
ΔGint-5 kcal/mol
Surface area9850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.572, 54.572, 148.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsBiological unit is one monomer of the observed dimer in the asymmetric unit. Determined by analytical ultracentrifugation.

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Components

#1: Protein Pleckstrin / Platelet p47 protein


Mass: 13020.819 Da / Num. of mol.: 2 / Fragment: PH2 Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLEK, P47 / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08567
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.106 Å3/Da / Density % sol: 40.495 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 0.1 M Tris, 0.05 M magnesium acetate, 6.0% glycerol, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 297.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 12, 2002 / Details: mirrors
RadiationMonochromator: Yale MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 13038 / Num. obs: 13038 / % possible obs: 94.2 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Biso Wilson estimate: 38.76 Å2 / Rmerge(I) obs: 0.05 / Χ2: 1.209
Reflection shellResolution: 2.1→2.14 Å / % possible obs: 70.5 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 3.24 / Num. measured obs: 459 / Num. unique all: 459 / Rsym value: 0.147 / Χ2: 0.798 / % possible all: 70.5

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Phasing

Phasing MRRfactor: 0.657 / Cor.coef. Fo:Fc: 0.461
Highest resolutionLowest resolution
Rotation3 Å44.11 Å
Translation3 Å44.11 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT1.6data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→25 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 898 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 914 6.6 %Random
Rwork0.236 ---
all0.244 13038 --
obs0.236 12111 87.8 %-
Solvent computationBsol: 81.695 Å2
Displacement parametersBiso mean: 50.129 Å2
Baniso -1Baniso -2Baniso -3
1--5.365 Å20 Å20 Å2
2---5.365 Å20 Å2
3---10.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1562 0 0 163 1725
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d1.34
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param

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