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- PDB-6ljf: Crystal structure of gelsolin G3 domain (calcium condition) -

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Basic information

Entry
Database: PDB / ID: 6ljf
TitleCrystal structure of gelsolin G3 domain (calcium 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 / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway ...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 / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / actin cap / sequestering of actin monomers / regulation of podosome assembly / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / actin filament capping / barbed-end actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / cell projection assembly / cardiac muscle cell contraction / podosome / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / phagocytosis, engulfment / cortical actin cytoskeleton / hepatocyte apoptotic process / cilium assembly / sarcoplasm / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / actin filament polymerization / central nervous system development / actin filament organization / protein destabilization / cellular response to type II interferon / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / blood microparticle / secretory granule lumen / 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: 1.5 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

Downloads & links

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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
Water5,405300
1
A: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4844
Polymers11,2601
Non-polymers2243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-11 kcal/mol
Surface area5900 Å2
MethodPISA
2
B: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3002
Polymers11,2601
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-11 kcal/mol
Surface area6050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.390, 41.810, 84.590
Angle α, β, γ (deg.)90.000, 105.232, 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, ammonium sulphate, calcium 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: Dec 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.5→40.809 Å / Num. obs: 31464 / % possible obs: 99.5 % / Redundancy: 4.858 % / Biso Wilson estimate: 22.829 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.069 / Χ2: 1.03 / Net I/σ(I): 16.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.594.780.678249710.7550.76198.5
1.59-1.74.8430.4213.3547500.8910.47399.4
1.7-1.844.8650.2565.744240.9530.28899.8
1.84-2.014.8720.13910.6541260.9860.15699.8
2.01-2.254.8850.08417.8537090.9940.09499.8
2.25-2.64.9070.05925.2632800.9970.06699.9
2.6-3.184.830.04134.2127780.9980.04799.9
3.18-4.484.9340.02451.9721960.9990.02799.6
4.48-40.8094.8630.0257.55123010.02299.4

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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: 1.5→40.809 Å / SU ML: 0.161 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.7057
RfactorNum. reflection% reflection
Rfree0.1835 1574 5 %
Rwork0.174 --
obs0.1744 31461 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.52 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1586 0 14 300 1900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00691666
X-RAY DIFFRACTIONf_angle_d0.83172246
X-RAY DIFFRACTIONf_chiral_restr0.0547238
X-RAY DIFFRACTIONf_plane_restr0.0051290
X-RAY DIFFRACTIONf_dihedral_angle_d23.5241632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.550.28981390.27852640X-RAY DIFFRACTION97.3
1.55-1.610.2621410.23682670X-RAY DIFFRACTION99.54
1.61-1.670.22961420.22542707X-RAY DIFFRACTION99.62
1.67-1.750.24531420.19992687X-RAY DIFFRACTION99.58
1.75-1.840.19221430.1942710X-RAY DIFFRACTION99.93
1.84-1.950.18411430.17182718X-RAY DIFFRACTION99.86
1.95-2.10.17981450.16822759X-RAY DIFFRACTION99.97
2.1-2.320.16381420.16512699X-RAY DIFFRACTION99.96
2.32-2.650.16451440.17582732X-RAY DIFFRACTION99.93
2.65-3.340.16411440.16812748X-RAY DIFFRACTION99.83
3.34-40.8090.17711490.15162817X-RAY DIFFRACTION99.66

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