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- PDB-1kcq: Human Gelsolin Domain 2 with a Cd2+ bound -

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Basic information

Entry
Database: PDB / ID: 1kcq
TitleHuman Gelsolin Domain 2 with a Cd2+ bound
ComponentsGELSOLIN
KeywordsSTRUCTURAL PROTEIN / alpha-beta structure / actin-binding protein / familial amyloidosis--Finnish type / cadmium binding / metal binding
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 / actin cap ...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 / barbed-end actin filament capping / actin filament depolymerization / actin filament capping / cell projection assembly / actin polymerization or depolymerization / cardiac muscle cell contraction / relaxation of cardiac muscle / Sensory processing of sound by outer hair cells of the cochlea / podosome / phagocytosis, engulfment / cortical actin cytoskeleton / hepatocyte apoptotic process / sarcoplasm / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / actin filament organization / central nervous system development / protein destabilization / cellular response to type II interferon / actin filament binding / lamellipodium / actin cytoskeleton / actin binding / secretory granule lumen / blood microparticle / 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 / cytoplasm / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKazmirski, S.L. / Isaacson, R.L. / An, C. / Buckle, A. / Johnson, C.M. / Daggett, V. / Fersht, A.R.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Loss of a metal-binding site in gelsolin leads to familial amyloidosis-Finnish type.
Authors: Kazmirski, S.L. / Isaacson, R.L. / An, C. / Buckle, A. / Johnson, C.M. / Daggett, V. / Fersht, A.R.
History
DepositionNov 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 / software / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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.ptnr1_symmetry / _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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)12,0435
Polymers11,5931
Non-polymers4504
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: GELSOLIN
hetero molecules

A: GELSOLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,08510
Polymers23,1862
Non-polymers8998
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1680 Å2
ΔGint-53 kcal/mol
Surface area10650 Å2
MethodPQS
Unit cell
Length a, b, c (Å)96.968, 26.525, 50.294
Angle α, β, γ (deg.)90.00, 121.19, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein GELSOLIN / ACTIN-DEPOLYMERIZING FACTOR / BREVIN / ADF / AGEL


Mass: 11592.965 Da / Num. of mol.: 1 / Fragment: DOMAIN 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P06396
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 400, cadmium chloride, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP at 290K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mM1reservoirCdCl2
2100 mMsodium acetate1reservoirpH4.6
320 %(v/v)PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1.2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 4, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.65→43.033 Å / Num. obs: 14799 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 5.2
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.174 / % possible all: 94.6
Reflection
*PLUS
Lowest resolution: 43 Å / Num. obs: 13093 / Num. measured all: 44277
Reflection shell
*PLUS
% possible obs: 94.6 % / Mean I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
MAR345data collection
SCALAdata scaling
AMoREphasing
X-PLORrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Residues 151-266 from PDB ENTRY 1D0N

1d0n


Resolution: 1.65→22.25 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 673 5 %Random
Rwork0.177 ---
all0.191 14799 --
obs0.18 13501 --
Displacement parametersBiso mean: 20.2 Å2
Refinement stepCycle: LAST / Resolution: 1.65→22.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms794 0 4 130 928
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.9
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.2 Å2
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.9

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