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- PDB-2xmf: Myosin 1e SH3 -

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Basic information

Entry
Database: PDB / ID: 2xmf
TitleMyosin 1e SH3
ComponentsMYOSIN 1E SH3
KeywordsMOTOR PROTEIN / SH3 DOMAIN
Function / homology
Function and homology information


podocyte development / glomerular basement membrane development / cuticular plate / glomerular filtration / clathrin-coated endocytic vesicle / post-embryonic hemopoiesis / myosin complex / hemopoiesis / cytoskeletal motor activity / brush border ...podocyte development / glomerular basement membrane development / cuticular plate / glomerular filtration / clathrin-coated endocytic vesicle / post-embryonic hemopoiesis / myosin complex / hemopoiesis / cytoskeletal motor activity / brush border / platelet-derived growth factor receptor signaling pathway / vasculogenesis / phosphatidylinositol binding / kidney development / adherens junction / endocytosis / actin filament binding / in utero embryonic development / cytoskeleton / calmodulin binding / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Unconventional myosin-Ie/If, SH3 domain / 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. ...Unconventional myosin-Ie/If, SH3 domain / 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. / IQ motif profile. / SH3 Domains / Kinesin motor domain superfamily / SH3 domain / Src homology 3 domains / SH3 type barrels. / 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
OCTANE 1,8-DIAMINE / Unconventional myosin-Ie / Myosin IE
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsEdwards, T. / Allsop, G. / Peckham, M.
CitationJournal: To be Published
Title: Myosin 1E SH3
Authors: Allsop, G. / Harris, S.A. / Peckham, M. / Edwards, T.
History
DepositionJul 27, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: MYOSIN 1E SH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8532
Polymers6,7081
Non-polymers1441
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.562, 55.560, 42.176
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2002-

HOH

21A-2022-

HOH

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Components

#1: Protein MYOSIN 1E SH3


Mass: 6708.439 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN, RESIDUES 239-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q3TLJ4, UniProt: E9Q634*PLUS
#2: Chemical ChemComp-DIA / OCTANE 1,8-DIAMINE / 1,8-DIAMINOOCTANE / OCTAMETHYLENEDIAMINE / 1,8-OCTANEDIAMINE


Mass: 144.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H20N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growDetails: 2.75 M AMPO4 PH 5.0, 5% DIAMINOOCTANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→35 Å / Num. obs: 7445 / % possible obs: 91.6 % / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.5

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→34.28 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.932 / SU B: 1.637 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22756 292 3.8 %RANDOM
Rwork0.17383 ---
obs0.17565 7445 90.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.851 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20 Å2
2--1.38 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms474 0 10 86 570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022495
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.969669
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.984559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.68725.41724
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8041577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.231152
X-RAY DIFFRACTIONr_chiral_restr0.0740.268
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02384
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.2219
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.2341
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.281
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6641.5306
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1812478
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1173222
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2034.5191
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.504 9 -
Rwork0.336 299 -
obs--49.36 %

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