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- PDB-1svy: SEVERIN DOMAIN 2, 1.75 ANGSTROM CRYSTAL STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1svy
TitleSEVERIN DOMAIN 2, 1.75 ANGSTROM CRYSTAL STRUCTURE
ComponentsSEVERIN
KeywordsACTIN-BINDING PROTEIN / CALCIUM-BINDING / CYTOSKELETON / GELSOLIN / SEVERIN / VILLIN / CALCIUM / PIP2
Function / homology
Function and homology information


actin filament severing activity / actin filament fragmentation / Neutrophil degranulation / actin filament severing / barbed-end actin filament capping / actin polymerization or depolymerization / actin filament bundle assembly / actin monomer binding / phagocytic vesicle / phosphatidylinositol-4,5-bisphosphate binding ...actin filament severing activity / actin filament fragmentation / Neutrophil degranulation / actin filament severing / barbed-end actin filament capping / actin polymerization or depolymerization / actin filament bundle assembly / actin monomer binding / phagocytic vesicle / phosphatidylinositol-4,5-bisphosphate binding / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / calcium ion binding / 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 speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.75 Å
AuthorsPuius, Y.A. / Fedorov, E.V. / Eichinger, L. / Sullivan, M. / Schleicher, M. / Almo, S.C.
Citation
Journal: Biochemistry / Year: 2000
Title: Mapping the functional surface of domain 2 in the gelsolin superfamily.
Authors: Puius, Y.A. / Fedorov, E.V. / Eichinger, L. / Schleicher, M. / Almo, S.C.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Structure of Severin Domain 2 in Solution
Authors: Schnuchel, A. / Wiltscheck, R. / Eichinger, L. / Schleicher, M. / Holak, T.A.
#2: Journal: Biochemistry / Year: 1992
Title: Characterization of Actin-and Lipid-Binding Domains in Severin, a Ca(2+)-Dependent F-Actin Fragmenting Protein
Authors: Eichinger, L. / Schleicher, M.
#3: Journal: J.Biol.Chem. / Year: 1988
Title: Severin, Gelsolin, and Villin Share a Homologous Sequence in Regions Presumed to Contain F-Actin Severing Domains
Authors: Andre, E. / Lottspeich, F. / Schleicher, M. / Noegel, A.
History
DepositionAug 10, 1998Processing site: BNL
Revision 1.0Aug 10, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SEVERIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3403
Polymers12,2771
Non-polymers632
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.352, 49.218, 62.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SEVERIN


Mass: 12276.842 Da / Num. of mol.: 1 / Fragment: DOMAIN 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: P10733
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 42 %
Crystal growpH: 8 / Details: pH 8.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.5 Msodium citrate1reservoir
2100 mMHEPES1reservoir
320 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.2
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Feb 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 10235 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.035 / Net I/σ(I): 30.9
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 9.9 / % possible all: 77.1
Reflection shell
*PLUS
% possible obs: 77.1 %

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Processing

Software
NameVersionClassification
PHASES-95model building
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASESV. 95phasing
X-PLOR3.851phasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.75→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: ISOTROPIC SOLVENT MASK
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1062 10.4 %RANDOM
Rwork0.1838 ---
obs0.1838 10177 93.1 %-
Displacement parametersBiso mean: 20.1 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms773 0 2 114 889
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.36
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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: 1.75→1.81 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3197 107 10.2 %
Rwork0.2736 939 -
obs--77.1 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2462
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.274

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