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- PDB-1yp5: Yeast Myo5 SH3 domain, tetragonal crystal form -

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Basic information

Entry
Database: PDB / ID: 1yp5
TitleYeast Myo5 SH3 domain, tetragonal crystal form
ComponentsMyosin-5 isoform
KeywordsCONTRACTILE PROTEIN / SH3 domain
Function / homology
Function and homology information


bipolar cellular bud site selection / myosin I complex / cellular bud / positive regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch localization / fungal-type cell wall organization / actin cortical patch / cell tip / mating projection tip / vesicle transport along actin filament ...bipolar cellular bud site selection / myosin I complex / cellular bud / positive regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch localization / fungal-type cell wall organization / actin cortical patch / cell tip / mating projection tip / vesicle transport along actin filament / response to osmotic stress / microfilament motor activity / exocytosis / response to salt stress / receptor-mediated endocytosis / cell periphery / actin filament organization / endocytosis / actin filament binding / actin cytoskeleton / vesicle / hydrolase activity / ATP binding / identical protein 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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsGonfloni, S. / Kursula, P. / Sacco, R. / Cesareni, G. / Wilmanns, M.
CitationJournal: To be Published
Title: Yeast Myo5 SH3 domain, tetragonal crystal form
Authors: Gonfloni, S. / Kursula, P. / Sacco, R. / Cesareni, G. / Wilmanns, M.
History
DepositionJan 29, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Sep 26, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / diffrn_radiation_wavelength / diffrn_source
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength_list
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myosin-5 isoform


Theoretical massNumber of molelcules
Total (without water)6,3761
Polymers6,3761
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.620, 34.620, 99.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Myosin-5 isoform


Mass: 6376.206 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: Q04439
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: sodium malonate, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.68→20 Å / Num. all: 7261 / Num. obs: 7261 / % possible obs: 96.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 26 Å2 / Rsym value: 0.053 / Net I/σ(I): 17.6
Reflection shellResolution: 1.68→1.75 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 824 / Rsym value: 0.422 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.089 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS REFINEMENT / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.109 / ESU R Free: 0.106 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22235 363 5 %RANDOM
Rwork0.18997 ---
all0.19156 7259 --
obs0.19156 7259 96.89 %-
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: 22.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2--1.01 Å20 Å2
3----2.02 Å2
Refinement stepCycle: LAST / Resolution: 1.68→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms450 0 0 60 510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022484
X-RAY DIFFRACTIONr_bond_other_d0.0020.02427
X-RAY DIFFRACTIONr_angle_refined_deg1.1621.993658
X-RAY DIFFRACTIONr_angle_other_deg0.73131011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.376561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.22724.11817
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.871579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.177151
X-RAY DIFFRACTIONr_chiral_restr0.0780.265
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02538
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0293
X-RAY DIFFRACTIONr_nbd_refined0.1890.264
X-RAY DIFFRACTIONr_nbd_other0.2410.2413
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.2219
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9872388
X-RAY DIFFRACTIONr_mcbond_other0.1762120
X-RAY DIFFRACTIONr_mcangle_it1.1633486
X-RAY DIFFRACTIONr_scbond_it1.5734229
X-RAY DIFFRACTIONr_scangle_it2.0225172
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.723 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.359 26
Rwork0.28 503
Refinement TLS params.Method: refined / Origin x: 2.189 Å / Origin y: 8.809 Å / Origin z: 9.266 Å
111213212223313233
T-0.1004 Å2-0.0134 Å2-0.0121 Å2--0.1153 Å2-0.0017 Å2---0.0508 Å2
L1.7072 °2-0.4604 °20.3479 °2-1.952 °20.5994 °2--5.1987 °2
S0.0201 Å °-0.1929 Å °0.0153 Å °-0.0388 Å °-0.0213 Å °0.1676 Å °-0.1039 Å °-0.3064 Å °0.0012 Å °

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