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- PDB-8brg: Crystal structure of She4 -

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Basic information

Entry
Database: PDB / ID: 8brg
TitleCrystal structure of She4
ComponentsKLLA0E16699p
KeywordsCHAPERONE / UNC-45 / UCS / myosin
Function / homologyUNC-45/Cro1/She4, central domain / Myosin-binding striated muscle assembly central / chaperone-mediated protein folding / Hsp90 protein binding / Armadillo-like helical / Armadillo-type fold / cytoplasm / KLLA0E16699p
Function and homology information
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGudino, R. / Arnese, R. / Meinhart, A. / Clausen, T.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: bioRxiv / Year: 2022
Title: UNC-45 assisted myosin folding depends on a conserved FX3HY motif implicated in Freeman Sheldon Syndrome
Authors: Vogel, A. / Arnese, R. / Gudino, R. / Sehr, D. / Bylicki, A. / Meinhart, A. / Clausen, T.
History
DepositionNov 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KLLA0E16699p


Theoretical massNumber of molelcules
Total (without water)75,8571
Polymers75,8571
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area30000 Å2
Unit cell
Length a, b, c (Å)129.510, 129.510, 77.190
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein KLLA0E16699p


Mass: 75856.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: She4 / Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: KLLA0_E16699g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CMY7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M MOPS/Hepes pH 7.5, 10% PEG 8000,20% Ethylene glycol, 0.03 mM CaCl2 and 0.03 mM MgCl2

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.976261 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976261 Å / Relative weight: 1
ReflectionResolution: 2.4→19.83 Å / Num. obs: 29424 / % possible obs: 99.74 % / Redundancy: 19.7 % / Biso Wilson estimate: 58.65 Å2 / CC1/2: 1 / Net I/σ(I): 19.71
Reflection shellResolution: 2.4→2.486 Å / Num. unique obs: 2908 / CC1/2: 0.589 / % possible all: 99.97

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MZU

5mzu


Resolution: 2.4→19.83 Å / SU ML: 0.3009 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.4881
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2555 1494 5.08 %
Rwork0.2064 27929 -
obs0.2089 29423 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.29 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5020 0 0 38 5058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00855093
X-RAY DIFFRACTIONf_angle_d1.02116899
X-RAY DIFFRACTIONf_chiral_restr0.0507832
X-RAY DIFFRACTIONf_plane_restr0.0078875
X-RAY DIFFRACTIONf_dihedral_angle_d14.7411913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.30811210.30192533X-RAY DIFFRACTION99.96
2.48-2.570.34781360.28232493X-RAY DIFFRACTION99.92
2.57-2.670.34631280.27292525X-RAY DIFFRACTION100
2.67-2.790.3061360.23952517X-RAY DIFFRACTION99.96
2.79-2.940.29821420.25042513X-RAY DIFFRACTION99.92
2.94-3.120.29611390.23752508X-RAY DIFFRACTION100
3.12-3.360.28681480.23482534X-RAY DIFFRACTION99.93
3.36-3.690.28491450.22632526X-RAY DIFFRACTION100
3.7-4.220.22711290.18922542X-RAY DIFFRACTION100
4.23-5.30.21311350.18222579X-RAY DIFFRACTION99.96
5.31-19.830.22421350.17242659X-RAY DIFFRACTION99.93
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)
12.73885352603-0.109943135389-0.5786218259142.65385010210.4064099124351.658135197980.1803576199250.357945915591-0.347591955909-0.3473033353920.00101398687471-0.4754191670990.152197590123-0.000573284406331-0.1831025293520.574291578850.09247470709260.1021820366840.677028684491-0.08381612518210.788323057524-69.2384166469-6.842034529610.6298256933
25.0865169330.661236780044-1.795488609714.25557046936-0.06509397872343.561807839470.196385226834-0.1903359040860.3211772852950.652126933577-0.03876319765640.397240171678-0.1242295052240.00892694088827-0.1577242083850.524357402690.002237675335640.09405833914050.4774984227910.03478638160150.418933738374-39.479799919615.15956776049.31240821718
36.355608086940.121266566138-0.8146470747156.27396446865-1.379959863943.23525504875-0.00695815029987-0.371884425151-0.5486024426810.03064171386470.0542298091732-0.2161729299470.2900471431950.0130767466754-0.07125891911910.4106262893950.03209772704010.007690059033560.4494793137380.0100068402910.374629920165-18.783121463113.6164752239-6.37822461156
44.96823894280.788114570812-1.059917919942.099684478360.1511887420241.63869841928-0.0729574230905-0.2461292879170.2678917648340.128089256480.119666758441-0.185009098812-0.0921967490270.205262410478-0.06184283099490.4271539794760.0199881390836-0.007525349229050.455216364183-0.008704601470380.344601616391-0.10299377990131.1306823064-14.3354554622
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 246 )1 - 2461 - 239
22chain 'A' and (resid 247 through 425 )247 - 425240 - 393
33chain 'A' and (resid 426 through 507 )426 - 507394 - 475
44chain 'A' and (resid 508 through 665 )508 - 665476 - 633

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