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- PDB-2drm: Acanthamoeba myosin I SH3 domain bound to Acan125 -

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Basic information

Entry
Database: PDB / ID: 2drm
TitleAcanthamoeba myosin I SH3 domain bound to Acan125
Components
  • 18-mer peptide from Acan125
  • Acanthamoeba Myosin IB
KeywordsCONTRACTILE PROTEIN / SH3 domain
Function / homology
Function and homology information


plasma membrane bounded cell projection / cellular component assembly / vesicle transport along actin filament / myosin complex / microfilament motor activity / cell leading edge / actin filament organization / endocytosis / actin filament binding / vesicle ...plasma membrane bounded cell projection / cellular component assembly / vesicle transport along actin filament / myosin complex / microfilament motor activity / cell leading edge / actin filament organization / endocytosis / actin filament binding / vesicle / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / SH3 Domains / Kinesin motor domain superfamily ...Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / SH3 Domains / Kinesin motor domain superfamily / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Myosin heavy chain IB
Similarity search - Component
Biological speciesAcanthamoeba (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsHoudusse, A. / Bahloul, A. / Ostap, E.M.
CitationJournal: To be Published
Title: The crystal structure of the SH3 domain of Acanthamoeba myosin IB bound to Acan125
Authors: Houdusse, A. / Bahloul, A. / Ostap, E.M. / Arold, S.
History
DepositionJun 9, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 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 1.4Oct 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 / 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 / _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:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acanthamoeba Myosin IB
B: Acanthamoeba Myosin IB
C: Acanthamoeba Myosin IB
D: Acanthamoeba Myosin IB
E: 18-mer peptide from Acan125
G: 18-mer peptide from Acan125
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,80218
Polymers29,6656
Non-polymers1,13712
Water4,846269
1
A: Acanthamoeba Myosin IB
B: Acanthamoeba Myosin IB
E: 18-mer peptide from Acan125
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,49710
Polymers14,8323
Non-polymers6657
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Acanthamoeba Myosin IB
D: Acanthamoeba Myosin IB
G: 18-mer peptide from Acan125
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3058
Polymers14,8323
Non-polymers4725
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.969, 37.861, 44.506
Angle α, β, γ (deg.)90.28, 90.11, 90.64
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Acanthamoeba Myosin IB / Myosin heavy chain IL


Mass: 6497.111 Da / Num. of mol.: 4 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba (eukaryote) / Genus: Acanthamoeba / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P19706
#2: Protein/peptide 18-mer peptide from Acan125


Mass: 1838.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in Acanthamoeba.
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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 % sol: 27.74 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.86 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.86 Å / Relative weight: 1
ReflectionResolution: 1.29→25 Å / Num. obs: 44074 / % possible obs: 89.4 % / Rmerge(I) obs: 0.02 / Χ2: 0.492 / Net I/σ(I): 16.6
Reflection shellResolution: 1.29→1.3 Å / Num. unique all: 675 / % possible all: 53.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.1.24refinement
PDB_EXTRACT2data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DRK

2drk


Resolution: 1.35→23.64 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.108 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20626 1977 5 %RANDOM
Rwork0.18575 ---
all0.19 ---
obs0.18678 37379 91.6 %-
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: 11.678 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0.02 Å2-0.1 Å2
2---0.64 Å2-0.02 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.35→23.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2075 0 64 269 2408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212192
X-RAY DIFFRACTIONr_bond_other_d0.0030.021834
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.9652993
X-RAY DIFFRACTIONr_angle_other_deg0.76734307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7845261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022439
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02401
X-RAY DIFFRACTIONr_nbd_refined0.2290.2412
X-RAY DIFFRACTIONr_nbd_other0.2580.22348
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0890.21235
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2232
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.236
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.2186
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.256
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6551.51328
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17622123
X-RAY DIFFRACTIONr_scbond_it1.633864
X-RAY DIFFRACTIONr_scangle_it2.4334.5870
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.268 139
Rwork0.216 2673
obs-2812

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