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- PDB-2v1q: Atomic-resolution structure of the yeast Sla1 SH3 domain 3 -

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Basic information

Entry
Database: PDB / ID: 2v1q
TitleAtomic-resolution structure of the yeast Sla1 SH3 domain 3
ComponentsCYTOSKELETON ASSEMBLY CONTROL PROTEIN SLA1
KeywordsSTRUCTURAL PROTEIN / STRUCTURAL GENOMICS / PHOSPHORYLATION / YEAST / SH3 DOMAIN / CYTOSKELETON / ACTIN-BINDING
Function / homology
Function and homology information


actin cytoskeleton-regulatory complex / SLAC complex / cargo adaptor activity / actin cortical patch assembly / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch / regulation of actin filament polymerization / cellular bud neck / mating projection tip ...actin cytoskeleton-regulatory complex / SLAC complex / cargo adaptor activity / actin cortical patch assembly / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch / regulation of actin filament polymerization / cellular bud neck / mating projection tip / ubiquitin binding / cell wall organization / endocytosis / actin binding / cell cortex / endosome membrane / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
SLA1 homology domain 1, SHD1 / Sla1, first SH3 domain / Sla1, third SH3 domain / SLA1 homology domain 1, SHD1 / Variant SH3 domain / SH3 Domains / Sterile alpha motif/pointed domain superfamily / SH3 domain / Src homology 3 domains / SH3 type barrels. ...SLA1 homology domain 1, SHD1 / Sla1, first SH3 domain / Sla1, third SH3 domain / SLA1 homology domain 1, SHD1 / Variant SH3 domain / SH3 Domains / Sterile alpha motif/pointed domain superfamily / SH3 domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
: / Actin cytoskeleton-regulatory complex protein SLA1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKursula, I. / Kursula, P. / Zou, P. / Lehmann, F. / Song, Y.H. / Wilmanns, M.
CitationJournal: To be Published
Title: Structural Genomics of Yeast SH3 Domains
Authors: Kursula, P. / Kursula, I. / Pinotsis, N. / Lehmann, F. / Zou, P. / Song, Y.H. / Wilmanns, M.
History
DepositionMay 29, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOSKELETON ASSEMBLY CONTROL PROTEIN SLA1
B: CYTOSKELETON ASSEMBLY CONTROL PROTEIN SLA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1166
Polymers13,6682
Non-polymers4494
Water3,495194
1
A: CYTOSKELETON ASSEMBLY CONTROL PROTEIN SLA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0523
Polymers6,8341
Non-polymers2182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CYTOSKELETON ASSEMBLY CONTROL PROTEIN SLA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0643
Polymers6,8341
Non-polymers2312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.940, 55.250, 85.290
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
11B-2087-

HOH

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Components

#1: Protein CYTOSKELETON ASSEMBLY CONTROL PROTEIN SLA1 / SLA1


Mass: 6833.769 Da / Num. of mol.: 2 / Fragment: SH3 DOMAIN 3, RESIDUES 357-413
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET24D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P32790
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 1.67 Å3/Da / Density % sol: 39 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. obs: 33200 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.4
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z9Z

1z9z


Resolution: 1.2→10 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.656 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.188 1747 5 %RANDOM
Rwork0.148 ---
obs0.151 33200 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--1.65 Å20 Å2
3----1.94 Å2
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms940 0 4 194 1138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221011
X-RAY DIFFRACTIONr_bond_other_d0.0020.02693
X-RAY DIFFRACTIONr_angle_refined_deg1.9491.9711372
X-RAY DIFFRACTIONr_angle_other_deg0.98531720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3015134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.92426.52246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.96315198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.842152
X-RAY DIFFRACTIONr_chiral_restr0.1260.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021125
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02185
X-RAY DIFFRACTIONr_nbd_refined0.2590.2164
X-RAY DIFFRACTIONr_nbd_other0.2020.2715
X-RAY DIFFRACTIONr_nbtor_refined0.180.2470
X-RAY DIFFRACTIONr_nbtor_other0.0940.2556
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2750.2126
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.270.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.992612
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.094997
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.7056422
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.48366
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: 1.2→1.23 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.26 125
Rwork0.216 2376

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