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- PDB-6lje: Crystal structure of gelsolin G3 domain (calcium and magnesium co... -

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Basic information

Entry
Database: PDB / ID: 6lje
TitleCrystal structure of gelsolin G3 domain (calcium and magnesium condition)
ComponentsGelsolin
KeywordsCYTOSOLIC PROTEIN / fragmin / gelsolin family protein / calcium regulation / actin filament severing
Function / homology
Function and homology information


striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / actin cap ...striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / actin cap / regulation of podosome assembly / myosin II binding / host-mediated suppression of symbiont invasion / actin filament severing / barbed-end actin filament capping / actin filament depolymerization / actin filament capping / actin polymerization or depolymerization / cell projection assembly / cardiac muscle cell contraction / relaxation of cardiac muscle / Sensory processing of sound by outer hair cells of the cochlea / podosome / phagocytosis, engulfment / cortical actin cytoskeleton / hepatocyte apoptotic process / sarcoplasm / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / actin filament organization / central nervous system development / protein destabilization / cellular response to type II interferon / actin filament binding / lamellipodium / actin cytoskeleton / actin binding / secretory granule lumen / blood microparticle / ficolin-1-rich granule lumen / amyloid fibril formation / Amyloid fiber formation / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsTakeda, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)16K17708 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)17K07373 Japan
CitationJournal: J.Muscle Res.Cell.Motil. / Year: 2020
Title: Novel inter-domain Ca2+-binding site in the gelsolin superfamily protein fragmin.
Authors: Takeda, S. / Fujiwara, I. / Sugimoto, Y. / Oda, T. / Narita, A. / Maeda, Y.
History
DepositionDec 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gelsolin
B: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7846
Polymers22,5202
Non-polymers2644
Water4,450247
1
A: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3923
Polymers11,2601
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-11 kcal/mol
Surface area6000 Å2
MethodPISA
2
B: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3923
Polymers11,2601
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-11 kcal/mol
Surface area5960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.900, 41.240, 84.590
Angle α, β, γ (deg.)90.000, 105.539, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Gelsolin / AGEL / Actin-depolymerizing factor / ADF / Brevin


Mass: 11259.854 Da / Num. of mol.: 2 / Fragment: UNP residues 297-397
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSN / Production host: Escherichia coli (E. coli) / References: UniProt: P06396
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.03 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG3350, ammonium sulphate, calcium chloride, magnesium chloride

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.4→40.751 Å / Num. obs: 37286 / % possible obs: 96.5 % / Redundancy: 5.107 % / Biso Wilson estimate: 24.303 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.058 / Χ2: 1.022 / Net I/σ(I): 15.58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.494.7740.8511.5358180.6860.95693.7
1.49-1.594.9170.4612.9555180.8950.51694.9
1.59-1.724.9930.2735.0652410.9560.30595.7
1.72-1.885.0590.1529.3348170.9850.1796.6
1.88-2.15.1420.08117.6644260.9960.0997.6
2.1-2.425.3560.05626.2639350.9970.06297.7
2.42-2.975.4760.04434.0133860.9980.04898.9
2.97-4.185.4460.03243.9426230.9990.03599.2
4.18-40.7515.4560.02947.4815220.9990.03299.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.15refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ffk

3ffk


Resolution: 1.4→40.75 Å / SU ML: 0.1666 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.9788
RfactorNum. reflection% reflection
Rfree0.1887 1865 5 %
Rwork0.1827 --
obs0.183 37274 96.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.79 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1586 0 14 247 1847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121678
X-RAY DIFFRACTIONf_angle_d1.21312266
X-RAY DIFFRACTIONf_chiral_restr0.1104245
X-RAY DIFFRACTIONf_plane_restr0.0079289
X-RAY DIFFRACTIONf_dihedral_angle_d26.94451016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.38431380.35722623X-RAY DIFFRACTION93.34
1.44-1.480.29861390.28312626X-RAY DIFFRACTION93.67
1.48-1.530.24361380.25972627X-RAY DIFFRACTION94.47
1.53-1.580.2391410.23022679X-RAY DIFFRACTION95.08
1.58-1.650.24351420.21622691X-RAY DIFFRACTION95.64
1.65-1.720.19391430.19222708X-RAY DIFFRACTION96.12
1.72-1.810.19941420.19012716X-RAY DIFFRACTION96.72
1.81-1.930.17931430.17932701X-RAY DIFFRACTION96.9
1.93-2.080.18291440.17252736X-RAY DIFFRACTION97
2.08-2.280.18991470.17232796X-RAY DIFFRACTION97.97
2.28-2.620.20081460.18692782X-RAY DIFFRACTION98.52
2.62-3.290.20081490.18332835X-RAY DIFFRACTION99.14
3.29-40.750.14851530.15742889X-RAY DIFFRACTION99.35

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