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- PDB-3fze: Structure of the 'minimal scaffold' (ms) domain of Ste5 that coca... -

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Basic information

Entry
Database: PDB / ID: 3fze
TitleStructure of the 'minimal scaffold' (ms) domain of Ste5 that cocatalyzes Fus3 phosphorylation by Ste7
ComponentsProtein STE5
KeywordsPROTEIN BINDING / alpha/beta/alpha / vWA-like fold (SCOP) / Cytoplasm / Pheromone response / Phosphoprotein
Function / homology
Function and homology information


mating projection tip membrane / pheromone-dependent signal transduction involved in conjugation with cellular fusion / invasive growth in response to glucose limitation / MAP-kinase scaffold activity / mating projection tip / negative regulation of MAPK cascade / phosphatidylinositol-4,5-bisphosphate binding / kinase binding / G-protein beta-subunit binding / positive regulation of protein phosphorylation ...mating projection tip membrane / pheromone-dependent signal transduction involved in conjugation with cellular fusion / invasive growth in response to glucose limitation / MAP-kinase scaffold activity / mating projection tip / negative regulation of MAPK cascade / phosphatidylinositol-4,5-bisphosphate binding / kinase binding / G-protein beta-subunit binding / positive regulation of protein phosphorylation / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Protein Ste5, Fus3-binding domain / Protein Ste5, Fus3-binding domain / Scaffold protein Ste5, Fus3-binding domain / Ste5, Fus3-binding domain superfamily / Scaffold protein Ste5, Fus3-binding region / Protein kinase Fus3-binding / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.601 Å
AuthorsGood, M.C. / Tang, G. / Singleton, J. / Remenyi, A. / Lim, W.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: The Ste5 scaffold directs mating signaling by catalytically unlocking the Fus3 MAP kinase for activation.
Authors: Good, M. / Tang, G. / Singleton, J. / Remenyi, A. / Lim, W.A.
History
DepositionJan 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein STE5


Theoretical massNumber of molelcules
Total (without water)22,5231
Polymers22,5231
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.803, 63.569, 69.091
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein STE5


Mass: 22523.375 Da / Num. of mol.: 1 / Fragment: UNP residues 593-786
Source method: isolated from a genetically manipulated source
Details: Expressed with N-terminal TEV-cleavable His6 tag. Cleaved tag for crystallization (leaving GS cloning mark at N-terminus)
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NUL3, STE5, YD8557.12, YDR103W / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS cells (Novagen) / References: UniProt: P32917
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: Mixed 10mg/mL protein 1:1 (vol:vol) with solution of 20% PEG3350, 0.1M citrate pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.111.11587
SYNCHROTRONALS 8.3.121.00556, 1.00949, 1.04796
Detector
TypeIDDetectorDate
ADSC QUANTUM Q315r1CCDSep 3, 2006
ADSC QUANTUM Q315r2CCDSep 9, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1KHOZU Double flat crystalSINGLE WAVELENGTHMx-ray1
2KHOZU Double flat crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.115871
21.005561
31.009491
41.047961
ReflectionResolution: 1.6→50 Å / Num. obs: 25696 / % possible obs: 92.4 % / Redundancy: 4.3 % / Rsym value: 0.046 / Net I/σ(I): 19.3
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 4 / Rsym value: 0.311 / % possible all: 93.9

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Processing

Software
NameVersionClassification
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.601→22.165 Å / SU ML: 0.21 / σ(F): 0.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2367 1224 5.05 %randomly chosen 5% of reflections
Rwork0.2086 ---
obs0.2101 24227 87.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.734 Å2 / ksol: 0.391 e/Å3
Refinement stepCycle: LAST / Resolution: 1.601→22.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1583 0 0 122 1705
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_deg0.952
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.601-1.6650.27661170.21762435243583
1.665-1.74080.24981320.21462595259590
1.7408-1.83250.21541570.20112640264092
1.8325-1.94730.31791440.27792376237683
1.9473-2.09750.23121370.21692725272593
2.0975-2.30840.24281300.20952368236881
2.3084-2.6420.25561460.20142861286197
2.642-3.32680.23821520.19822960296099
3.3268-22.16670.18731090.18842043204366
Refinement TLS params.Method: refined / Origin x: 12.2571 Å / Origin y: 10.9675 Å / Origin z: 11.0925 Å
111213212223313233
T0.0518 Å20.0273 Å2-0.0031 Å2-0.1182 Å20.0311 Å2--0.0927 Å2
L1.8206 °2-0.1174 °20.443 °2-1.4543 °2-0.6455 °2--1.9614 °2
S-0.1275 Å °-0.0399 Å °0.0849 Å °0.1819 Å °0.1698 Å °0.0764 Å °-0.1019 Å °-0.3003 Å °-0.0668 Å °
Refinement TLS groupSelection details: chain A

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