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- PDB-3opb: Crystal structure of She4p -

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Basic information

Entry
Database: PDB / ID: 3opb
TitleCrystal structure of She4p
ComponentsSWI5-dependent HO expression protein 4
KeywordsPROTEIN BINDING / HEAT and ARM fold / Myosin folding and function / myosin binding protein
Function / homology
Function and homology information


mating type switching / intracellular mRNA localization / myosin binding / actin cytoskeleton organization / identical protein binding / cytoplasm
Similarity search - Function
Leucine-rich Repeat Variant - #100 / UNC-45/Cro1/She4, central domain / Myosin-binding striated muscle assembly central / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
SWI5-dependent HO expression protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsShi, H. / Blobel, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: UNC-45/CRO1/She4p (UCS) protein forms elongated dimer and joins two myosin heads near their actin binding region.
Authors: Shi, H. / Blobel, G.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 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: SWI5-dependent HO expression protein 4
B: SWI5-dependent HO expression protein 4


Theoretical massNumber of molelcules
Total (without water)175,7622
Polymers175,7622
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-28 kcal/mol
Surface area69330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.022, 149.937, 158.483
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 SWI5-dependent HO expression protein 4


Mass: 87880.984 Da / Num. of mol.: 2 / Mutation: C4S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SHE4, YOR035C, OR26.26 / Production host: Escherichia coli (E. coli) / References: UniProt: P51534
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE UNK SEQUENCE CORRESPONDING TO RESIDUES 422-440 HAS THE FOLLOWING CHEMICAL COMPOSITION: SNGSSQSINDLKNYADLKG
Sequence detailsRESIDUES RANGE 422-440 HAVE POOR DEFINED ELECTRON DENSITY. ONLY 5 RESIDUES CORRESPONDING TO REGION ...RESIDUES RANGE 422-440 HAVE POOR DEFINED ELECTRON DENSITY. ONLY 5 RESIDUES CORRESPONDING TO REGION 426-430 OF CHAIN A COULD BE ASSIGNED TO THE MAIN CHAIN

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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: 2.84 Å3/Da / Density % sol: 56.69 %
Crystal growTemperature: 285 K / Method: evaporation / pH: 6.5
Details: 200 mM Na citrate, 20% (w/v) PEG 3350, 10 mM DTT, pH 6.5, EVAPORATION, temperature 285K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONNSLS X12C1
SYNCHROTRONNSLS X29A2
Detector
TypeIDDetector
ADSC QUANTUM 2101CCD
ADSC QUANTUM 3152CCD
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.9→45 Å / Num. all: 47498 / Num. obs: 45409 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.063
Reflection shellResolution: 2.9→3 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.79

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Processing

Software
NameClassification
CBASSdata collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.9→43 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.296 2783 random
Rwork0.231 --
all0.32 45119 -
obs0.32 38886 -
Refinement stepCycle: LAST / Resolution: 2.9→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11874 0 0 141 12015
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.381
X-RAY DIFFRACTIONc_bond_d0.0081

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