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

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Basic information

Entry
Database: PDB / ID: 6qbp
Titlestructure of the core domaine of Knr4, an intrinsically disordered protein from Saccharomyces cerevisiae - mutant 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: 2.4 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 S203D
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 / 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)61,8982
Polymers61,8982
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 area900 Å2
ΔGint-5 kcal/mol
Surface area20740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.949, 102.949, 93.139
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: ASN / Beg label comp-ID: ASN / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 84 - 342 / Label seq-ID: 12 - 270

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: 30949.148 Da / Num. of mol.: 2 / Mutation: 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

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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: 2.3 Å3/Da / Density % sol: 46.56 %
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: ID23-1 / Wavelength: 0.976256 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976256 Å / Relative weight: 1
ReflectionResolution: 2.4→89.17 Å / Num. obs: 21807 / % possible obs: 99.1 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rrim(I) all: 0.043 / Rsym value: 0.036 / Net I/σ(I): 17.6
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1 / Num. unique obs: 3415 / CC1/2: 0.371 / Rrim(I) all: 1.115 / Rsym value: 0.888 / % possible all: 97.2

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Processing

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

5j1b


Resolution: 2.4→45.09 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 20.724 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.219 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21863 1116 5.1 %RANDOM
Rwork0.19069 ---
obs0.19216 20705 99.02 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 57.227 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.4→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3451 0 0 0 3451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0143572
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173082
X-RAY DIFFRACTIONr_angle_refined_deg1.0281.6484862
X-RAY DIFFRACTIONr_angle_other_deg0.7911.6367222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5995424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04423.971204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.31815554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.241515
X-RAY DIFFRACTIONr_chiral_restr0.0520.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024017
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02691
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_it1.1785.6451720
X-RAY DIFFRACTIONr_mcbond_other1.1775.6441719
X-RAY DIFFRACTIONr_mcangle_it1.9928.4542136
X-RAY DIFFRACTIONr_mcangle_other1.9928.4552137
X-RAY DIFFRACTIONr_scbond_it1.1535.8111851
X-RAY DIFFRACTIONr_scbond_other1.1535.811849
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9958.6552726
X-RAY DIFFRACTIONr_long_range_B_refined3.45564.5723896
X-RAY DIFFRACTIONr_long_range_B_other3.45464.5813897
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6871 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.399→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 67 -
Rwork0.374 1428 -
obs--93.03 %
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)
18.2454-0.26241.98613.48290.03143.67340.30530.2519-1.2095-0.04620.05780.55440.9162-0.1281-0.36310.47280.001-0.1510.1550.09670.497911.4529.18770.741
27.0576-0.28461.36092.25990.10664.27310.14721.2933-0.1686-0.3619-0.0080.09340.39860.8409-0.13920.29170.1642-0.07540.43240.00570.097224.03919.65364.698
315.7429.2638-1.239614.54043.9135.6103-0.12840.20240.63540.78940.35280.18020.0260.0066-0.22440.24360.1144-0.05710.26510.06320.094726.34322.8478.713
410.35670.84241.17783.5481-0.30722.46960.06090.18170.05640.1770.07160.19650.0879-0.0568-0.13240.19560.0824-0.0470.13510.0710.112415.58823.51870.574
510.87671.2285-1.02764.35581.171311.33140.09020.55060.2168-0.4356-0.18621.03740.0012-0.54780.0960.16850.1155-0.11630.34960.1660.45720.58827.71561.949
612.55640.56499.168.65587.68612.8692-0.02610.08160.8643-0.1098-0.0782-0.3795-0.1104-0.04060.10430.18610.10360.02430.15030.10920.600614.0832.7870.408
77.3237-0.16520.35073.56110.22873.62510.2431-0.7345-0.98040.5156-0.1008-0.02850.4454-0.2593-0.14220.2179-0.1176-0.08250.13450.1390.161745.18110.92494.707
87.0449-0.50131.21123.0570.99114.89750.15610.11540.4457-0.0191-0.22280.2059-0.4563-0.24810.06670.12320.00410.00620.08610.0110.054538.76725.04884.824
99.4059-1.32590.89592.19320.16172.94610.12160.1239-0.27940.11830.1341-0.4493-0.21780.266-0.25570.1064-0.0682-0.05530.1051-0.01670.155356.43918.88386.684
101.3113-0.3723.37231.96841.853324.59580.09640.25170.261-0.0319-0.2271-0.2431-0.0162-0.34090.13070.0746-0.01570.0640.18070.04310.147854.62821.03773.527
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A84 - 150
2X-RAY DIFFRACTION2A151 - 252
3X-RAY DIFFRACTION3A253 - 263
4X-RAY DIFFRACTION4A264 - 293
5X-RAY DIFFRACTION5A294 - 326
6X-RAY DIFFRACTION6A327 - 342
7X-RAY DIFFRACTION7B84 - 166
8X-RAY DIFFRACTION8B167 - 263
9X-RAY DIFFRACTION9B264 - 326
10X-RAY DIFFRACTION10B327 - 346

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