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- PDB-2aso: Structure of Rabbit Actin In Complex With Sphinxolide B -

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Basic information

Entry
Database: PDB / ID: 2aso
TitleStructure of Rabbit Actin In Complex With Sphinxolide B
ComponentsActin, alpha skeletal muscle
KeywordsSTRUCTURAL PROTEIN / actin / sphinxolide B / marine macrolide / toxin / filament capping / filament severing
Function / homology
Function and homology information


cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament ...cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family ...ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / SPHINXOLIDE B / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAllingham, J.S. / Zampella, A. / D'Auria, M.V. / Rayment, I.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structures of microfilament destabilizing toxins bound to actin provide insight into toxin design and activity
Authors: Allingham, J.S. / Zampella, A. / D'Auria, M.V. / Rayment, I.
History
DepositionAug 23, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_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_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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _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:
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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3834
Polymers41,8761
Non-polymers1,5073
Water5,657314
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.182, 54.989, 103.520
Angle α, β, γ (deg.)90.00, 92.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-651-

HOH

21A-756-

HOH

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Components

#1: Protein Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41875.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-SPX / SPHINXOLIDE B / N-((4R,5R,9S,10S,11S,E)-11-((3R,5Z,7Z,11S,12S,13Z,15R,17S,18S,19Z,21S,23S,24R,25S,29S)-17,29-DIHYDROXY-3,15,21,23-TETRAMETHOXY-5,12,18,24-TETRAMETHYL-9,27-DIOXO-10,26-DIOXABICYCLO[23.3.1]NONACOSA-1(28),5,7,13,19-PENTAEN-11-YL)-4,10-DIMETHOXY-5,9-DIMETHYL-6-OXODODEC-1-ENYL)-N-METHYLFORMAMIDE


Mass: 960.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C53H85NO14
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 1.87 Å3/Da / Density % sol: 37.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100mM Na/MES/Acetate, pH 5.5, 12% methyl ether poly(ethylene glycol) 5000, 100mM CaCl2, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9641 Å
DetectorType: SBC-2 / Detector: CCD / Date: Mar 28, 2004 / Details: Rosenbaum-Rock monochromators and mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9641 Å / Relative weight: 1
ReflectionResolution: 1.7→35 Å / Num. obs: 36176 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 29.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 3.8 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QZ5

1qz5


Resolution: 1.7→35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.381 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21347 1792 5 %RANDOM
Rwork0.17298 ---
all0.193 35870 --
obs0.17511 34079 99.37 %-
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: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å20 Å2-0.15 Å2
2---0.63 Å20 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 100 314 3162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212912
X-RAY DIFFRACTIONr_bond_other_d0.0020.022668
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.9973960
X-RAY DIFFRACTIONr_angle_other_deg1.59436202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6275358
X-RAY DIFFRACTIONr_chiral_restr0.1230.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023156
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02558
X-RAY DIFFRACTIONr_nbd_refined0.2230.2773
X-RAY DIFFRACTIONr_nbd_other0.2430.23301
X-RAY DIFFRACTIONr_nbtor_other0.1180.21940
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2181
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2920.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3380.229
X-RAY DIFFRACTIONr_mcbond_it0.7611.51792
X-RAY DIFFRACTIONr_mcangle_it1.43222904
X-RAY DIFFRACTIONr_scbond_it2.29131120
X-RAY DIFFRACTIONr_scangle_it3.7074.51055
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.265 119
Rwork0.224 2379

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