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- PDB-2fh1: C-terminal half of gelsolin soaked in low calcium at pH 4.5 -

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Basic information

Entry
Database: PDB / ID: 2fh1
TitleC-terminal half of gelsolin soaked in low calcium at pH 4.5
ComponentsGelsolin
KeywordsCONTRACTILE PROTEIN / gelsolin / calcium
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 / Resolution: 1.55 Å
AuthorsChumnarnsilpa, S. / Loonchanta, A. / Xue, B. / Choe, H. / Urosev, D. / Wang, H. / Burtnick, L.D. / Robinson, R.C.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Calcium ion exchange in crystalline gelsolin
Authors: Chumnarnsilpa, S. / Loonchanta, A. / Xue, B. / Choe, H. / Urosev, D. / Wang, H. / Lindberg, U. / Burtnick, L.D. / Robinson, R.C.
History
DepositionDec 23, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 23, 2018Group: Data collection / Category: diffrn_source / struct_biol / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gelsolin
B: Gelsolin
C: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,64712
Polymers113,2863
Non-polymers3619
Water21,0781170
1
A: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8824
Polymers37,7621
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8824
Polymers37,7621
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8824
Polymers37,7621
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.822, 90.320, 156.299
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a monomer. There are 3 biological units in the asymmetric unit (chains A, B and C)

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Components

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


Mass: 37762.098 Da / Num. of mol.: 3 / Fragment: C-terminal half domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: modified pGEx-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 Blue / References: UniProt: P06396
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1170 / 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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 277 K / Method: micro batch under oil / pH: 4.5
Details: PEG 8000, pH 4.5, micro batch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.957 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 25, 2004
RadiationMonochromator: Single Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.957 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 164723 / Num. obs: 164723 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.55→1.59 Å / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.1.24refinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→19.69 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.398 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.214 8728 5 %RANDOM
Rwork0.191 ---
all0.193 164723 --
obs0.193 164723 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.485 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.55→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7496 0 9 1170 8675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0217669
X-RAY DIFFRACTIONr_bond_other_d0.0030.026784
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.94410409
X-RAY DIFFRACTIONr_angle_other_deg0.83315821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6135960
X-RAY DIFFRACTIONr_chiral_restr0.1050.21106
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028672
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021545
X-RAY DIFFRACTIONr_nbd_refined0.240.21616
X-RAY DIFFRACTIONr_nbd_other0.2540.27979
X-RAY DIFFRACTIONr_nbtor_other0.0840.24452
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2805
X-RAY DIFFRACTIONr_metal_ion_refined0.0760.245
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3080.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3420.2146
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.250
X-RAY DIFFRACTIONr_mcbond_it0.9191.54783
X-RAY DIFFRACTIONr_mcangle_it1.62227654
X-RAY DIFFRACTIONr_scbond_it2.30932886
X-RAY DIFFRACTIONr_scangle_it3.5124.52755
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.277 596
Rwork0.24 12050
obs-12646

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