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- PDB-2q0r: Structure of Pectenotoxin-2 Bound to Actin -

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Basic information

Entry
Database: PDB / ID: 2q0r
TitleStructure of Pectenotoxin-2 Bound to Actin
ComponentsActin
KeywordsSTRUCTURAL PROTEIN / pectenotoxin / actin / anti-tumor / filament capping / natural product / cytotoxin / macrolide
Function / homology
Function and homology information


cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / 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 / PECTENOTOXIN-2 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAllingham, J.S. / Miles, C.O. / Rayment, I.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: A structural basis for regulation of actin polymerization by pectenotoxins.
Authors: Allingham, J.S. / Miles, C.O. / Rayment, I.
History
DepositionMay 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 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_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3877
Polymers41,8631
Non-polymers1,5256
Water6,954386
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.437, 56.856, 105.747
Angle α, β, γ (deg.)90.000, 90.160, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-935-

HOH

21A-976-

HOH

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Components

#1: Protein Actin / / Alpha-actin-1


Mass: 41862.613 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.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-PXT / PECTENOTOXIN-2


Mass: 857.034 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H68O14
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.13 Å3/Da / Density % sol: 42.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Na/MES/acetate, pH 5.5, 15% methyl ether poly(ethylene glycol) 5000, 10% hexanediol, 30 mM CaCl2, and 1 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.96411 Å
DetectorType: SBC / Detector: CCD / Date: Aug 6, 2006
Details: Rosenbaum-Rock double-crystal monochromator: Water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96411 Å / Relative weight: 1
ReflectionResolution: 1.7→45 Å / Num. obs: 37755 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.04 / Χ2: 0.882 / Net I/σ(I): 14.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.109 / Mean I/σ(I) obs: 9.5 / Num. unique all: 3595 / Χ2: 0.618 / % possible all: 93.4

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Phasing

Phasing MRRfactor: 0.483 / Cor.coef. Fo:Fc: 0.536
Highest resolutionLowest resolution
Rotation2 Å26.44 Å
Translation2 Å26.44 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-3000data collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ASO

2aso


Resolution: 1.7→45 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.831 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1887 5 %RANDOM
Rwork0.168 ---
obs0.17 37752 96.98 %-
all-157276 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.099 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å2-0.02 Å2
2---0.92 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 96 386 3262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222951
X-RAY DIFFRACTIONr_bond_other_d0.0050.022664
X-RAY DIFFRACTIONr_angle_refined_deg1.7722.0034041
X-RAY DIFFRACTIONr_angle_other_deg1.32136180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4985372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83823.947114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71515473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1021515
X-RAY DIFFRACTIONr_chiral_restr0.0870.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023243
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02578
X-RAY DIFFRACTIONr_nbd_refined0.220.2595
X-RAY DIFFRACTIONr_nbd_other0.1870.22761
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21459
X-RAY DIFFRACTIONr_nbtor_other0.0890.21650
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2246
X-RAY DIFFRACTIONr_metal_ion_refined0.0790.213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3930.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.229
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0760.24
X-RAY DIFFRACTIONr_mcbond_it0.8221.51858
X-RAY DIFFRACTIONr_mcbond_other0.21.5735
X-RAY DIFFRACTIONr_mcangle_it1.26922925
X-RAY DIFFRACTIONr_scbond_it2.06931256
X-RAY DIFFRACTIONr_scangle_it3.0114.51109
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 140 -
Rwork0.168 2444 -
obs-2584 90.86 %

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