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- PDB-6qbo: structure of the core domaine of Knr4, an intrinsically disordere... -

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Basic information

Entry
Database: PDB / ID: 6qbo
Titlestructure of the core domaine of Knr4, an intrinsically disordered protein from Saccharomyces cerevisiae - mutant S203A
ComponentsCell wall assembly regulator SMI1
KeywordsSIGNALING PROTEIN / cell-wall integrity / stress response / beta-glucan synthesis
Function / homology
Function and homology information


regulation of fungal-type cell wall biogenesis / fungal-type cell wall beta-glucan biosynthetic process / incipient cellular bud site / cellular bud neck / mating projection tip / regulation of mitotic cell cycle / cell wall organization / DNA binding / nucleus
Similarity search - Function
Knr4/Smi1 family / : / SMI1 / KNR4 family (SUKH-1) / Knr4/Smi1-like domain / SMI1 / KNR4 family / Knr4/Smi1-like domain superfamily
Similarity search - Domain/homology
Cell wall assembly regulator SMI1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsRamos, N. / Batista, M. / Francois, J.M. / Mourey, L. / Maveyraud, L. / Zerbib, D.
CitationJournal: To Be Published
Title: structure of the core domaine of Knr4, an intrinsically disordered protein from Saccharomyces cerevisiae - mutant S203A
Authors: Ramos, N. / Batista, M. / Francois, J.M. / Mourey, L. / Maveyraud, L. / Zerbib, D.
History
DepositionDec 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell wall assembly regulator SMI1
B: Cell wall assembly regulator SMI1


Theoretical massNumber of molelcules
Total (without water)61,8102
Polymers61,8102
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, dimer is observed at high concentration in SAXS and SEC-MALS experiments
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-3 kcal/mol
Surface area20840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.104, 103.104, 93.565
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A4 - 260
2010B4 - 260

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Components

#1: Protein Cell wall assembly regulator SMI1 / Killer toxin-resistance protein 4


Mass: 30905.141 Da / Num. of mol.: 2 / Mutation: S203A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SMI1, KNR4, KTR4, YGR229C, G8553 / Production host: Escherichia coli (E. coli) / References: UniProt: P32566

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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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / Details: PEG 3000 - 6000 15-24 % (w/v) Bicine buffer 0.1 M / PH range: 8.0 - 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072274 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072274 Å / Relative weight: 1
ReflectionResolution: 2.75→45.2 Å / Num. obs: 14760 / % possible obs: 99.8 % / Redundancy: 5.7 % / CC1/2: 0.999 / Rrim(I) all: 0.074 / Rsym value: 0.067 / Net I/σ(I): 14.4
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 765 / CC1/2: 0.325 / Rrim(I) all: 1.488 / Rsym value: 1.334 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5j1b

5j1b


Resolution: 2.75→45.19 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 32.207 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R: 3.687 / ESU R Free: 0.298 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21355 741 5 %RANDOM
Rwork0.18525 ---
obs0.1867 14013 99.79 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 73.368 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å20 Å2
3----0.78 Å2
Refinement stepCycle: 1 / Resolution: 2.75→45.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 0 0 3472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0143583
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173080
X-RAY DIFFRACTIONr_angle_refined_deg1.1051.6474882
X-RAY DIFFRACTIONr_angle_other_deg0.831.647206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1675432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44624.365197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.77115543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3121512
X-RAY DIFFRACTIONr_chiral_restr0.0550.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024048
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02696
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6637.2421749
X-RAY DIFFRACTIONr_mcbond_other1.6637.2411748
X-RAY DIFFRACTIONr_mcangle_it2.72410.8492174
X-RAY DIFFRACTIONr_mcangle_other2.72310.852175
X-RAY DIFFRACTIONr_scbond_it1.6427.3791834
X-RAY DIFFRACTIONr_scbond_other1.6427.381835
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.70511.0032709
X-RAY DIFFRACTIONr_long_range_B_refined4.30883.6864000
X-RAY DIFFRACTIONr_long_range_B_other4.30883.6984001
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6892 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.75→2.822 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 48 -
Rwork0.338 1022 -
obs--98.35 %
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)
14.01631.9754-0.8665.58140.4663.4926-0.1313-0.09340.06970.28740.1803-0.45670.11970.0288-0.04910.10090.0693-0.06020.0534-0.03580.06697.89950.36155.541
23.89252.39531.23276.22121.76443.7812-0.19090.3837-0.4334-0.42840.3559-0.05320.16740.5762-0.16510.13440.0201-0.05110.34220.01210.1108-8.52123.36836.128
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 267
2X-RAY DIFFRACTION2B4 - 261

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