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- PDB-4e7w: Structure of GSK3 from Ustilago maydis -

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Basic information

Entry
Database: PDB / ID: 4e7w
TitleStructure of GSK3 from Ustilago maydis
ComponentsGlycogen Synthase Kinase 3
KeywordsTRANSFERASE / GSK3 / Kinase / pTyr195
Function / homologyPhosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta / :
Function and homology information
Biological speciesUstilago maydis (corn smut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsGruetter, C. / Rauh, D.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: Targeting GSK3 from Ustilago maydis: Type-II Kinase Inhibitors as Potential Antifungals.
Authors: Grutter, C. / Simard, J.R. / Mayer-Wrangowski, S.C. / Schreier, P.H. / Perez-Martin, J. / Richters, A. / Getlik, M. / Gutbrod, O. / Braun, C.A. / Beck, M.E. / Rauh, D.
History
DepositionMar 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogen Synthase Kinase 3


Theoretical massNumber of molelcules
Total (without water)44,7981
Polymers44,7981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)151.420, 151.420, 67.430
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Glycogen Synthase Kinase 3


Mass: 44797.781 Da / Num. of mol.: 1 / Mutation: Delta(S59-K70)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ustilago maydis (corn smut) / Strain: 521 / FGSC 9021 / Gene: UM00560.1 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q4PH53, non-specific serine/threonine protein kinase
Has protein modificationY

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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: 4.98 Å3/Da / Density % sol: 75.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8-12% (w/v) EtOH, 1.5 M NaCl, 40 mM SrCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9826 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 30, 2007 / Details: Dynamicall bendable mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9826 Å / Relative weight: 1
ReflectionResolution: 3.3→45 Å / Num. all: 13660 / Num. obs: 13635 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.19 % / Biso Wilson estimate: 99.254 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.52
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
3.3-3.46.350.6653728911481148100
3.4-3.50.5783.4364071023100
3.5-3.90.267.0219710313699.9
3.9-4.420.10515.43160592562100
4.42-6.20.05228.21224603638100
6.2-90.02844.728461140999.8
9-150.0264.4319656699.6
150.01960.6277715389.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.3 Å39.94 Å
Translation3.3 Å39.94 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1I09

1i09


Resolution: 3.3→39.94 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.85 / WRfactor Rfree: 0.2803 / WRfactor Rwork: 0.227 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7598 / SU B: 25.73 / SU ML: 0.412 / SU R Cruickshank DPI: 1.1913 / SU Rfree: 0.4734 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.191 / ESU R Free: 0.473 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2969 819 6 %RANDOM
Rwork0.2409 ---
obs0.2442 13635 100 %-
all-13660 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 168.42 Å2 / Biso mean: 121.6046 Å2 / Biso min: 80 Å2
Baniso -1Baniso -2Baniso -3
1-3.47 Å21.73 Å20 Å2
2--3.47 Å20 Å2
3----5.2 Å2
Refinement stepCycle: LAST / Resolution: 3.3→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 0 0 2871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222937
X-RAY DIFFRACTIONr_angle_refined_deg1.0581.9863984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1015359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31223.566129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.5915520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7571522
X-RAY DIFFRACTIONr_chiral_restr0.0740.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212207
X-RAY DIFFRACTIONr_mcbond_it0.9251.51806
X-RAY DIFFRACTIONr_mcangle_it1.19222939
X-RAY DIFFRACTIONr_scbond_it0.54831131
X-RAY DIFFRACTIONr_scangle_it1.0114.51045
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 61 -
Rwork0.353 951 -
all-1012 -
obs--100 %

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