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- PDB-1jo8: Structural analysis of the yeast actin binding protein Abp1 SH3 domain -

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Basic information

Entry
Database: PDB / ID: 1jo8
TitleStructural analysis of the yeast actin binding protein Abp1 SH3 domain
ComponentsACTIN BINDING PROTEIN
KeywordsSTRUCTURAL PROTEIN / SH3 domain Actin-binding-protein
Function / homology
Function and homology information


protein localization to actin cortical patch / positive regulation of Arp2/3 complex-mediated actin nucleation / site of polarized growth / actin cortical patch assembly / actin cortical patch / regulation of actin filament polymerization / mating projection tip / barbed-end actin filament capping / cortical actin cytoskeleton / actin filament binding ...protein localization to actin cortical patch / positive regulation of Arp2/3 complex-mediated actin nucleation / site of polarized growth / actin cortical patch assembly / actin cortical patch / regulation of actin filament polymerization / mating projection tip / barbed-end actin filament capping / cortical actin cytoskeleton / actin filament binding / cell cortex / cytoplasm
Similarity search - Function
Fungal actin-binding protein 1, second SH3 domain / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains ...Fungal actin-binding protein 1, second SH3 domain / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Actin-binding protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsFazi, B. / Cope, M.J. / Douangamath, A. / Ferracuti, S. / Schirwitz, K. / Zucconi, A. / Drubin, D.G. / Wilmanns, M. / Cesareni, G. / Castagnoli, L.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Unusual binding properties of the SH3 domain of the yeast actin-binding protein Abp1: structural and functional analysis.
Authors: Fazi, B. / Cope, M.J. / Douangamath, A. / Ferracuti, S. / Schirwitz, K. / Zucconi, A. / Drubin, D.G. / Wilmanns, M. / Cesareni, G. / Castagnoli, L.
History
DepositionJul 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_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

Downloads & links

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Assembly

Deposited unit
A: ACTIN BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8553
Polymers6,6631
Non-polymers1922
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.080, 38.155, 59.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein ACTIN BINDING PROTEIN / Abp1p / actin-binding protein ABP1 /


Mass: 6663.082 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pLysS / References: UniProt: P15891
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Ammonium sulfate, bis-tris-propane, pH 8.0, VAPOR DIFFUSION, SITTING DROP at 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13.2 Mammonium sulfate1reservoir
2100 mMBis-Tris propane1reservoirpH8.0
312 mg/mlAbp1-SH31drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.842 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 2000
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.842 Å / Relative weight: 1
ReflectionResolution: 1.3→25 Å / Num. all: 57575 / Num. obs: 56424 / % possible obs: 98 % / Redundancy: 4.1 % / Biso Wilson estimate: 9.8 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.3
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 4 / Num. unique all: 617 / % possible all: 88.6
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 13742 / % possible obs: 98 % / Num. measured all: 56424
Reflection shell
*PLUS
% possible obs: 88.6 %

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CKA

1cka


Resolution: 1.3→17.51 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.17785 680 5 %RANDOM
Rwork0.14352 ---
all0.1451 13027 --
obs0.14512 13027 98.05 %-
Displacement parametersBiso mean: 8.742 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.3→17.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms505 0 13 131 649
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_mcbond_it1.1371.5
X-RAY DIFFRACTIONp_mcangle_it1.8332
X-RAY DIFFRACTIONp_scbond_it2.2143
X-RAY DIFFRACTIONp_scangle_it3.2744.5
X-RAY DIFFRACTIONp_bond_d0.0110
X-RAY DIFFRACTIONp_angle_deg1.7141.9
X-RAY DIFFRACTIONp_angle_d1.7141.9
X-RAY DIFFRACTIONp_planar_d0.0090
X-RAY DIFFRACTIONp_chiral_restr0.1180.02
X-RAY DIFFRACTIONp_singtor_nbd4.9723
X-RAY DIFFRACTIONp_multtor_nbd13.76115
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 38 4.4 %
Rwork0.171 866 -
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.194 / Rfactor Rwork: 0.171 / Total num. of bins used: 20

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