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- PDB-1d4x: Crystal Structure of Caenorhabditis Elegans Mg-ATP Actin Complexe... -

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Basic information

Entry
Database: PDB / ID: 1d4x
TitleCrystal Structure of Caenorhabditis Elegans Mg-ATP Actin Complexed with Human Gelsolin Segment 1 at 1.75 A resolution.
Components
  • C. ELEGANS ACTIN 1/3
  • GELSOLIN
KeywordsCONTRACTILE PROTEIN / ACTIN / GELSOLIN S1 / C.ELEGANS / MG-ATP
Function / homologyGelsolin / Actins and actin-related proteins signature. / Gelsolin repeat / Actins signature 1. / Actin, conserved site / Villin/Gelsolin / Actins signature 2. / Actin family / Caspase-mediated cleavage of cytoskeletal proteins / Neutrophil degranulation ...Gelsolin / Actins and actin-related proteins signature. / Gelsolin repeat / Actins signature 1. / Actin, conserved site / Villin/Gelsolin / Actins signature 2. / Actin family / Caspase-mediated cleavage of cytoskeletal proteins / Neutrophil degranulation / ADF-H/Gelsolin-like domain superfamily / Actin / Actin/actin-like conserved site / Gelsolin-like domain / Amyloid fiber formation / regulation of receptor clustering / regulation of establishment of T cell polarity / striated muscle atrophy / positive regulation of keratinocyte apoptotic process / renal protein absorption / regulation of plasma membrane raft polarization / positive regulation of protein processing in phagocytic vesicle / actin cap / positive regulation of actin nucleation / sequestering of actin monomers / regulation of podosome assembly / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / myosin II binding / sarcoplasm / negative regulation of viral entry into host cell / actin filament severing / actin nucleation / barbed-end actin filament capping / tissue regeneration / embryo development ending in birth or egg hatching / oligodendrocyte development / actin filament capping / cortical actin cytoskeleton / response to folic acid / cortical actin cytoskeleton organization / podosome / hepatocyte apoptotic process / cilium assembly / striated muscle thin filament / regulation of cell adhesion / mitotic cytokinesis / phagocytic vesicle / amyloid fibril formation / actin filament reorganization / actin filament polymerization / phosphatidylinositol-mediated signaling / cellular response to interferon-gamma / ruffle / protein destabilization / phagocytosis, engulfment / cellular response to cadmium ion / actin cytoskeleton / actin filament binding / lamellipodium / actin binding / secretory granule lumen / response to ethanol / cytoskeleton / ficolin-1-rich granule lumen / blood microparticle / aging / myelin sheath / focal adhesion / cellular protein metabolic process / positive regulation of gene expression / neutrophil degranulation / calcium ion binding / perinuclear region of cytoplasm / extracellular space / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytosol / cytoplasm / Gelsolin / Actin-1 / Actin-3
Function and homology information
Specimen sourceCaenorhabditis elegans (roundworm)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 1.75 Å resolution
AuthorsVorobiev, S. / Ono, S. / Almo, S.C.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2003
Title: The structure of nonvertebrate actin: implications for the ATP hydrolytic mechanism.
Authors: Vorobiev, S. / Strokopytov, B. / Drubin, D.G. / Frieden, C. / Ono, S. / Condeelis, J. / Rubenstein, P.A. / Almo, S.C.
#1: Journal: Nature / Year: 1993
Title: Structure of gelsolin segment 1-actin complex and mechanosm of filament severing
Authors: McLaughlin, P.J. / Gooch, J.T. / Mannherz, H.-G. / Weeds, A.G.
#2: Journal: Nature / Year: 1990
Title: Atomic structure of the actin:DNase I complex
Authors: Kabsch, W. / Mannherz, H.-G. / Suck, D. / Pai, E.F. / Holmes, K.C.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 6, 1999 / Release: May 2, 2001
RevisionDateData content typeGroupProviderType
1.0May 2, 2001Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C. ELEGANS ACTIN 1/3
G: GELSOLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6437
Polyers55,9122
Non-polymers7325
Water9,044502
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3520
ΔGint (kcal/M)-49
Surface area (Å2)20500
MethodPISA
2
A: C. ELEGANS ACTIN 1/3
G: GELSOLIN
hetero molecules

A: C. ELEGANS ACTIN 1/3
G: GELSOLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,28614
Polyers111,8234
Non-polymers1,46310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area (Å2)9440
ΔGint (kcal/M)-111
Surface area (Å2)38920
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)177.820, 68.989, 56.593
Angle α, β, γ (deg.)90.00, 104.15, 90.00
Int Tables number5
Space group name H-MC 1 2 1

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Components

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Protein/peptide , 2 types, 2 molecules AG

#1: Protein/peptide C. ELEGANS ACTIN 1/3


Mass: 41710.492 Da / Num. of mol.: 1 / Source: (gene. exp.) Caenorhabditis elegans (roundworm) / Genus: Caenorhabditis / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P10983, UniProt: P0DM41*PLUS
#2: Protein/peptide GELSOLIN /


Mass: 14201.010 Da / Num. of mol.: 1 / Fragment: SEGMENT 1 / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P06396

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Non-polymers , 6 types, 507 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Formula: SO4 / Sulfate
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#6: Chemical ChemComp-SO2 / SULFUR DIOXIDE


Mass: 64.064 Da / Num. of mol.: 1 / Formula: O2S / Sulfur dioxide
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Formula: Ca / Calcium
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Formula: H2O / Water

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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: 3.01 / Density percent sol: 59.14 %
Crystal growTemp: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 MM TRIS-HCL, PH 8.0, 2 MM MG-ATP, 1.60 M LI2SO4,, VAPOR DIFFUSION, HANGING DROP, temperature 293K
components of the solutions
*PLUS

Crystal ID: 1

IDConcCommon nameSol IDChemical formulaDetails
22 mMTris-HCldrop
32 mMATPdrop
44 mMdropMgCl2
50.5 mMEGTAdrop
61 mMdropNaN3
71.55 MreservoirLiSO4
82 mMMg2+-ATPreservoir
90.5 mMEGTAreservoir
1gelsolindrop1:1.25 stoichiometry
100.1 MHEPESreservoir

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: NSLS BEAMLINE X9B / Synchrotron site: NSLS / Beamline: X9B / Wavelength: 1.072
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Collection date: Jan 1, 1999
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 17.041 Å2 / D resolution high: 1.75 Å / D resolution low: 25 Å / Number all: 64713 / Number obs: 64713 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.041 / NetI over sigmaI: 24.2 / Redundancy: 3.91 % / Percent possible obs: 96.9
Reflection shellRmerge I obs: 0.102 / Highest resolution: 1.75 Å / Lowest resolution: 1.81 Å / Redundancy: 2.57 % / Percent possible all: 88.3
Reflection shell
*PLUS
Percent possible obs: 88.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefineR Free selection details: RANDOM / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: R. A. ENGH AND R. HUBER
Least-squares processR factor R free: 0.233 / R factor R work: 0.1986 / R factor all: 0.2307 / R factor obs: 0.2307 / Highest resolution: 1.75 Å / Lowest resolution: 23.2 Å / Number reflection R free: 2533 / Number reflection all: 64712 / Number reflection obs: 64711 / Percent reflection obs: 4
Refine hist #LASTHighest resolution: 1.75 Å / Lowest resolution: 23.2 Å
Number of atoms included #LASTProtein: 3822 / Nucleic acid: 0 / Ligand: 41 / Solvent: 502 / Total: 4365
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d1.624
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
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
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Displacement parameters
*PLUS
B iso mean: 24.14 Å2
Least-squares process
*PLUS
R factor R work: 0.199 / Lowest resolution: 25 Å
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.434

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