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- PDB-1ruw: Crystal structure of the SH3 domain from S. cerevisiae Myo3 -

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Basic information

Entry
Database: PDB / ID: 1ruw
TitleCrystal structure of the SH3 domain from S. cerevisiae Myo3
ComponentsMyosin-3 isoform
KeywordsCONTRACTILE PROTEIN / SH3 domain / Myo3 / yeast / high-throughput / structural genomics
Function / homology
Function and homology information


bipolar cellular bud site selection / myosin I complex / positive regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch localization / fungal-type cell wall organization / actin cortical patch / cell tip / vesicle transport along actin filament / response to osmotic stress / microfilament motor activity ...bipolar cellular bud site selection / myosin I complex / positive regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch localization / fungal-type cell wall organization / actin cortical patch / cell tip / vesicle transport along actin filament / response to osmotic stress / microfilament motor activity / myosin binding / exocytosis / cell periphery / actin filament organization / endocytosis / actin filament binding / actin cytoskeleton / vesicle / hydrolase activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Fungal myosin-I, 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. / SH3 Domains ...Fungal myosin-I, 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. / 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
IMIDAZOLE / Myosin-3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKursula, P. / Kursula, I. / Lehmann, F. / Song, Y.H. / Wilmanns, M.
CitationJournal: To be Published
Title: Crystal structure of the SH3 domain from S. cerevisiae Myo3
Authors: Kursula, P. / Kursula, I. / Lehmann, F. / Song, Y.H. / Wilmanns, M.
History
DepositionDec 12, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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-3 isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6582
Polymers7,5881
Non-polymers691
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.330, 48.000, 78.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2588-

HOH

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Components

#1: Protein Myosin-3 isoform / Myo3


Mass: 7588.495 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P36006
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 1.98 Å3/Da / Density % sol: 37.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Ammonium sulfate, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 27, 2003
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 7396 / Num. obs: 7337 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.084 / Rsym value: 0.061 / Net I/σ(I): 12.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.367 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→10 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.242 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.145 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24611 511 7 %RANDOM
Rwork0.17279 ---
all0.17759 ---
obs0.17759 6782 99.36 %-
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: 19.649 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å20 Å2
2---1.82 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms578 0 5 106 689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022599
X-RAY DIFFRACTIONr_bond_other_d0.0030.02547
X-RAY DIFFRACTIONr_angle_refined_deg1.0181.989810
X-RAY DIFFRACTIONr_angle_other_deg0.64131298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.696568
X-RAY DIFFRACTIONr_chiral_restr0.0770.288
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02629
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02115
X-RAY DIFFRACTIONr_nbd_refined0.1830.2133
X-RAY DIFFRACTIONr_nbd_other0.2480.2642
X-RAY DIFFRACTIONr_nbtor_other0.0820.2355
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.270
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2620.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.228
X-RAY DIFFRACTIONr_mcbond_it2.5123355
X-RAY DIFFRACTIONr_mcangle_it3.5835587
X-RAY DIFFRACTIONr_scbond_it4.1745244
X-RAY DIFFRACTIONr_scangle_it5.1656223
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 34
Rwork0.22 454

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