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- PDB-1nph: Gelsolin Domains 4-6 in Active, Actin Free Conformation Identifie... -

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Basic information

Entry
Database: PDB / ID: 1nph
TitleGelsolin Domains 4-6 in Active, Actin Free Conformation Identifies Sites of Regulatory Calcium Ions
ComponentsGelsolin
KeywordsPROTEIN BINDING / BETA SHEET
Function / homology
Function and homology information


Caspase-mediated cleavage of cytoskeletal proteins / 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 ...Caspase-mediated cleavage of cytoskeletal proteins / 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 / actin filament depolymerization / actin filament capping / cardiac muscle cell contraction / podosome / relaxation of cardiac muscle / phagocytosis, engulfment / hepatocyte apoptotic process / sarcoplasm / cilium assembly / phagocytic vesicle / vesicle-mediated transport / response to muscle stretch / Neutrophil degranulation / actin filament polymerization / protein destabilization / cellular response to type II interferon / actin filament binding / lamellipodium / actin cytoskeleton organization / amyloid fibril formation / calcium ion binding / extracellular space / extracellular region / nucleus / plasma membrane / cytosol
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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKolappan, S. / Gooch, J.T. / Weeds, A.G. / McLaughlin, P.J.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Gelsolin Domains 4-6 in Active, Actin-Free Conformation Identifies Sites of Regulatory Calcium Ions
Authors: Kolappan, S. / Gooch, J.T. / Weeds, A.G. / McLaughlin, P.J.
History
DepositionJan 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_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.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_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

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Assembly

Deposited unit
A: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4343
Polymers36,3531
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.520, 122.520, 82.723
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Gelsolin / Actin-depolymerizing factor


Mass: 36353.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: GSN OR GSB / Plasmid: pET derivative pMW172 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13020
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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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: 4.52 Å3/Da / Density % sol: 72.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mMTris-HCl1reservoirpH8.0
215 %(w/v)PEG80001reservoir
30.1 mM1reservoirCaCl2
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 31, 2002 / Details: mirror, Monochromator
RadiationMonochromator: Liquid gallium cooled, bent, triangular, si 111 optimised for 1.488 (11.7 asymmetric cut)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 3→87.7 Å / Num. obs: 13119 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 5.2
Reflection shellResolution: 3→3.16 Å / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.313
Reflection
*PLUS
Num. obs: 13141 / % possible obs: 99.4 % / Rmerge(I) obs: 0.12
Reflection shell
*PLUS
Rmerge(I) obs: 0.31

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DB0

1db0
PDB Unreleased entry


Resolution: 3→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.299 659 -RANDOM
Rwork0.247 ---
all-13085 --
obs-12876 98.4 %-
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 2 0 2454
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_bond_d0.01
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3-3.110.43600.4131169116996
3.11-3.230.402700.342115496
3.23-3.380.336600.308117897
3.38-3.560.329630.286120598
3.56-3.780.361720.283119399
3.78-4.070.343710.269121199
4.07-4.480.257670.192123999
4.48-5.120.225660.1981255100
5.12-6.430.268590.2431279100
6.43-250.256710.211133499
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.298 / Rfactor Rwork: 0.2452
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.01
LS refinement shell
*PLUS
Rfactor Rfree: 0.43

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