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

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Basic information

Entry
Database: PDB / ID: 6qbr
Titlestructure of the core domaine of Knr4, an intrinsically disordered protein from Saccharomyces cerevisiae - mutant S200D, S203D
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: 2.15 Å
AuthorsGuillien, M. / 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 S200D, S203D
Authors: Guillien, M. / 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)61,9542
Polymers61,9542
Non-polymers00
Water1,13563
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 area1190 Å2
ΔGint-4 kcal/mol
Surface area21210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.380, 102.380, 92.336
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:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 83 - 343 / Label seq-ID: 11 - 271

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 30977.160 Da / Num. of mol.: 2 / Mutation: S200D, S203D
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
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: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.15→45 Å / Num. obs: 29991 / % possible obs: 99.5 % / Redundancy: 5.2 % / CC1/2: 0.997 / Rrim(I) all: 0.068 / Rsym value: 0.062 / Net I/σ(I): 13.3
Reflection shellResolution: 2.15→2.28 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4716 / CC1/2: 0.52 / Rrim(I) all: 0.959 / Rsym value: 0.806 / % possible all: 97

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Processing

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

5j1b


Resolution: 2.15→44.81 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 13.247 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.17 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21852 1550 5.2 %RANDOM
Rwork0.19085 ---
obs0.19228 28440 99.47 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 87.995 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20.36 Å20 Å2
2--0.72 Å20 Å2
3----2.35 Å2
Refinement stepCycle: 1 / Resolution: 2.15→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3526 0 0 63 3589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0143634
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173114
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.6484954
X-RAY DIFFRACTIONr_angle_other_deg0.9281.647282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0985442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14523.9200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27815546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0511515
X-RAY DIFFRACTIONr_chiral_restr0.0640.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024125
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02707
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_it2.09561786
X-RAY DIFFRACTIONr_mcbond_other2.0965.9971785
X-RAY DIFFRACTIONr_mcangle_it3.3038.9722222
X-RAY DIFFRACTIONr_mcangle_other3.3038.9752223
X-RAY DIFFRACTIONr_scbond_it2.2916.1591848
X-RAY DIFFRACTIONr_scbond_other2.296.1541846
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5939.1482732
X-RAY DIFFRACTIONr_long_range_B_refined5.59469.5134094
X-RAY DIFFRACTIONr_long_range_B_other5.59569.4544088
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 7083 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.146→2.202 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 120 -
Rwork0.332 1978 -
obs--93.49 %
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)
11.48811.1321-0.47461.58890.36091.5024-0.0188-0.0231-0.01950.00610.1687-0.1765-0.0475-0.128-0.14990.2560.0139-0.05280.2137-0.02360.24087.75849.76855.185
22.30411.92481.44381.76591.60412.70180.01310.4658-0.2699-0.04140.5105-0.1299-0.02230.5869-0.52360.0353-0.0166-0.12920.3706-0.09860.6317-8.7222.86835.583
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A83 - 347
2X-RAY DIFFRACTION2B83 - 343

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