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- PDB-3ffn: Crystal structure of calcium-free human gelsolin -

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Basic information

Entry
Database: PDB / ID: 3ffn
TitleCrystal structure of calcium-free human gelsolin
ComponentsGelsolin
KeywordsActin binding Protein / Gelsolin / Actin / Ca-dependent / Actin capping / Actin-binding / Alternative initiation / Amyloid / Amyloidosis / Calcium / Cytoplasm / Cytoskeleton / Disease mutation / Disulfide bond / Phosphoprotein / Polymorphism / Secreted
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 / sarcoplasm / 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 / 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 / Resolution: 3 Å
AuthorsChumnarnsilpa, S. / Robinson, R.C. / Burtnick, L.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Ca2+ binding by domain 2 plays a critical role in the activation and stabilization of gelsolin.
Authors: Nag, S. / Ma, Q. / Wang, H. / Chumnarnsilpa, S. / Lee, W.L. / Larsson, M. / Kannan, B. / Hernandez-Valladares, M. / Burtnick, L.D. / Robinson, R.C.
History
DepositionDec 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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


Theoretical massNumber of molelcules
Total (without water)171,5972
Polymers171,5972
Non-polymers00
Water1,856103
1
A: Gelsolin


Theoretical massNumber of molelcules
Total (without water)85,7981
Polymers85,7981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Gelsolin


Theoretical massNumber of molelcules
Total (without water)85,7981
Polymers85,7981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)170.887, 170.887, 152.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-794-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A43 - 73
2111B43 - 73
1211A378 - 411
2211B378 - 411
1311A733 - 750
2311B733 - 750
1411A284 - 371
2411B284 - 371
1511A82 - 109
2511B82 - 109
1611A116 - 124
2611B116 - 124
1711A126 - 149
2711B126 - 149
1811A159 - 253
2811B159 - 253
1911A259 - 276
2911B259 - 276
1121A537 - 732
2121B537 - 732
1221A412 - 420
2221B412 - 420
1321A422 - 453
2321B422 - 453
1421A460 - 525
2421B460 - 525

NCS ensembles :
ID
1
2

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Components

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


Mass: 85798.398 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.24 Å3/Da / Density % sol: 62.01 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% glycerol, 100 mM Bis-Tris HCl, 1.5M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 45666 / % possible obs: 100 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 27.188
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
3-3.118.10.338100
3.11-3.238.20.258100
3.23-3.388.30.195100
3.38-3.568.30.145100
3.56-3.788.40.106100
3.78-4.078.50.07899.9
4.07-4.488.60.0699.9
4.48-5.128.70.056100
5.12-6.438.60.068100
6.43-258.10.05199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 3→24.84 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.873 / SU B: 16.037 / SU ML: 0.303 / Cross valid method: THROUGHOUT / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2359 5.2 %RANDOM
Rwork0.22 ---
obs0.222 43262 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.94 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 3→24.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11297 0 0 103 11400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211549
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.94815650
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32551447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0224.46556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.641151905
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4181574
X-RAY DIFFRACTIONr_chiral_restr0.0910.21666
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028964
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.24575
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.27651
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2406
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7721.57346
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.379211503
X-RAY DIFFRACTIONr_scbond_it1.46734794
X-RAY DIFFRACTIONr_scangle_it2.5554.54147
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
12683tight positional0.040.05
22341tight positional0.040.05
12683tight thermal0.090.5
22341tight thermal0.090.5
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 191 -
Rwork0.259 3065 -
obs--99.85 %

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