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- PDB-2dyn: DYNAMIN (PLECKSTRIN HOMOLOGY DOMAIN) (DYNPH) -

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Basic information

Entry
Database: PDB / ID: 2dyn
TitleDYNAMIN (PLECKSTRIN HOMOLOGY DOMAIN) (DYNPH)
ComponentsDYNAMIN
KeywordsSIGNAL TRANSDUCTION / MOTOR PROTEIN / PHOSPHOLIPID BINDING / PROTEIN BINDING
Function / homology
Function and homology information


clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / presynaptic endocytic zone membrane / dynamin GTPase / chromaffin granule / regulation of vesicle size / Toll Like Receptor 4 (TLR4) Cascade / Retrograde neurotrophin signalling / Formation of annular gap junctions ...clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / presynaptic endocytic zone membrane / dynamin GTPase / chromaffin granule / regulation of vesicle size / Toll Like Receptor 4 (TLR4) Cascade / Retrograde neurotrophin signalling / Formation of annular gap junctions / endosome organization / Gap junction degradation / photoreceptor ribbon synapse / membrane coat / Recycling pathway of L1 / phosphatidylinositol-3,4,5-trisphosphate binding / endocytic vesicle / EPH-ephrin mediated repulsion of cells / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / MHC class II antigen presentation / photoreceptor inner segment / receptor-mediated endocytosis / cell projection / modulation of chemical synaptic transmission / protein homooligomerization / receptor internalization / endocytosis / GDP binding / : / presynapse / Clathrin-mediated endocytosis / microtubule binding / protein homotetramerization / microtubule / GTPase activity / glutamatergic synapse / synapse / GTP binding / protein kinase binding / protein homodimerization activity / RNA binding / extracellular exosome / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain ...Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / 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 / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR WITH ANOMALOUS SCATTERING / Resolution: 2.3 Å
AuthorsTimm, D.E.
CitationJournal: Nat.Struct.Biol. / Year: 1994
Title: Crystal structure of the pleckstrin homology domain from dynamin.
Authors: Timm, D. / Salim, K. / Gout, I. / Guruprasad, L. / Waterfield, M. / Blundell, T.
History
DepositionJul 21, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DYNAMIN
B: DYNAMIN


Theoretical massNumber of molelcules
Total (without water)28,8612
Polymers28,8612
Non-polymers00
Water1,20767
1
A: DYNAMIN
B: DYNAMIN
x 8


Theoretical massNumber of molelcules
Total (without water)230,88616
Polymers230,88616
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Unit cell
Length a, b, c (Å)86.020, 86.020, 137.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.847437, -0.116183, -0.518027), (-0.174077, -0.861006, 0.477877), (-0.501546, 0.495147, 0.709423)
Vector: 58.76, 31.514, 8.652)

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Components

#1: Protein DYNAMIN / PH DOMAIN / DYNPH


Mass: 14430.390 Da / Num. of mol.: 2 / Fragment: PLECKSTRIN HOMOLOGY (PH) DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: EXPRESSED AS GST-FUSION PROTEIN, CLEAVED WITH THROMBIN
Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 BLUE / References: UniProt: Q05193
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growpH: 6.1
Details: PROTEIN (10-20 MG/ML) WAS CRYSTALLIZED FROM 10-30% PEG 8000, 0.2 M AMMONIUM SULFATE, PH 6.1 BY THE HANGING DROP VAPOR DIFFUSION METHOD
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-30 %PEG80001reservoir
20.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1995 / Details: SYNCHROTRON
RadiationMonochromator: SYNCHROTRON / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.3→24.31 Å / Num. obs: 11759 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 6.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 5.1 / Rsym value: 0.144 / % possible all: 99.3

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR WITH ANOMALOUS SCATTERING
Resolution: 2.3→24.31 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: POSTERIORI / σ(F): 2
Details: A BULK SOLVENT MASK WAS APPLIED IN XPLOR 3.1. RESIDUES WITH OCCUPANCY OF 0.00 ARE INCLUDED IN THE MODEL, BUT ARE NOT DEFINED BY THE ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.296 924 8 %RANDOM
Rwork0.2139 ---
obs0.2139 11755 99.5 %-
Displacement parametersBiso mean: 38.5 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 0 66 1924
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.476
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.21
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.993
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
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3864 109 7.8 %
Rwork0.3351 1287 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2966
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.215
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.993

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