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- PDB-1va7: Yeast Myo3 SH3 domain, triclinic crystal form -

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Basic information

Entry
Database: PDB / ID: 1va7
TitleYeast Myo3 SH3 domain, triclinic crystal form
ComponentsMyosin-3 isoform
KeywordsCONTRACTILE PROTEIN / Structural genomics / SH3 domain
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 / reticulophagy / 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 / reticulophagy / response to osmotic stress / microfilament motor activity / myosin binding / exocytosis / actin filament organization / cell periphery / endocytosis / actin filament binding / actin cytoskeleton / 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 / 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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKursula, P. / Lehmann, F. / Song, Y.H. / Wilmanns, M.
CitationJournal: To be Published
Title: High-throughput structural genomics of yeast SH3 domains
Authors: Kursula, P. / Lehmann, F. / Song, Y.H. / Wilmanns, M.
History
DepositionFeb 12, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 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 / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Myosin-3 isoform
B: Myosin-3 isoform
C: Myosin-3 isoform
D: Myosin-3 isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7666
Polymers30,5824
Non-polymers1842
Water00
1
A: Myosin-3 isoform


Theoretical massNumber of molelcules
Total (without water)7,6461
Polymers7,6461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myosin-3 isoform


Theoretical massNumber of molelcules
Total (without water)7,6461
Polymers7,6461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Myosin-3 isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7382
Polymers7,6461
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Myosin-3 isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7382
Polymers7,6461
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.800, 48.750, 48.840
Angle α, β, γ (deg.)60.70, 70.74, 70.60
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 1 / Auth seq-ID: 3 - 61 / Label seq-ID: 3 - 61

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
Detailseach chain is an independent biological unit

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Components

#1: Protein
Myosin-3 isoform / Myo3


Mass: 7645.547 Da / Num. of mol.: 4 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / References: UniProt: P36006
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

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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: 2.67 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: sodium citrate, glycerol, pH 7.5, 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: 0.8115 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8115 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 6221 / Num. obs: 6221 / % possible obs: 96.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 33 Å2 / Rsym value: 0.106 / Net I/σ(I): 7.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 609 / Rsym value: 0.406 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RUW

1ruw


Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.846 / SU B: 24.02 / SU ML: 0.436 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS parameters used / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R Free: 0.484 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28017 311 5 %RANDOM
Rwork0.23625 ---
all0.23831 6220 --
obs0.23831 6220 97.69 %-
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: 6.195 Å2
Baniso -1Baniso -2Baniso -3
1--1.86 Å2-0.64 Å2-1.53 Å2
2---0.6 Å26.61 Å2
3----2.58 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 12 0 1994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222054
X-RAY DIFFRACTIONr_bond_other_d0.0020.021786
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.9852784
X-RAY DIFFRACTIONr_angle_other_deg0.78934222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8445252
X-RAY DIFFRACTIONr_chiral_restr0.0730.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022248
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02398
X-RAY DIFFRACTIONr_nbd_refined0.1780.2307
X-RAY DIFFRACTIONr_nbd_other0.2410.21795
X-RAY DIFFRACTIONr_nbtor_other0.0860.21149
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.223
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.26
X-RAY DIFFRACTIONr_mcbond_it0.1751.51280
X-RAY DIFFRACTIONr_mcangle_it0.28522060
X-RAY DIFFRACTIONr_scbond_it0.4083774
X-RAY DIFFRACTIONr_scangle_it0.5624.5724
Refine LS restraints NCS

Ens-ID: 1 / Number: 860 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.030.05
2Btight positional0.030.05
3Ctight positional0.030.05
4Dtight positional0.030.05
1Atight thermal0.050.5
2Btight thermal0.050.5
3Ctight thermal0.050.5
4Dtight thermal0.050.5
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.422 23
Rwork0.357 440
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.4311-1.2325-0.74243.4952-0.53432.9893-0.3105-0.38920.3789-0.19550.3015-0.5001-0.12720.24810.0090.2812-0.0072-0.0340.2407-0.12050.23372.2494-0.62190.2925
211.986-0.32820.73861.3493-2.56872.4651-0.25890.3459-0.4322-0.03830.1702-0.37410.50620.36850.08870.4084-0.07980.02440.1738-0.19960.2414-17.161-8.19-13.0476
37.96962.27551.31162.8190.5799.1717-0.09070.0107-0.1716-0.7223-0.00220.3216-0.6493-0.36310.09290.4170.0151-0.04170.1349-0.04060.2569-29.51340.4357-28.4765
412.0048-2.7139-0.54515.53021.099710.41220.0045-0.08650.23851.00150.21580.26740.7593-0.6864-0.22030.4399-0.0636-0.00080.0766-0.03190.2228-10.2545-9.34515.6622
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 703 - 70
2X-RAY DIFFRACTION2BB3 - 703 - 70
3X-RAY DIFFRACTION3CC3 - 623 - 62
4X-RAY DIFFRACTION3CE71
5X-RAY DIFFRACTION4DD3 - 623 - 62
6X-RAY DIFFRACTION4DF71

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