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- PDB-8okf: WD repeat containing protein 5 (WDR5)- PER2 peptide -

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Basic information

Entry
Database: PDB / ID: 8okf
TitleWD repeat containing protein 5 (WDR5)- PER2 peptide
Components
  • Glutathione S-transferase class-mu 26 kDa isozyme,WD repeat domain 5
  • PER2 peptide
KeywordsCIRCADIAN CLOCK PROTEIN / WD40 repeat / peptide complex
Function / homology
Function and homology information


: / MLL3/4 complex / Set1C/COMPASS complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / regulation of tubulin deacetylation / regulation of cell division / regulation of embryonic development / MLL1 complex ...: / MLL3/4 complex / Set1C/COMPASS complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / regulation of tubulin deacetylation / regulation of cell division / regulation of embryonic development / MLL1 complex / glutathione transferase / glutathione transferase activity / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / methylated histone binding / skeletal system development / gluconeogenesis / regulation of cell cycle / negative regulation of transcription by RNA polymerase II
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / WD repeat domain 5 / Glutathione S-transferase class-mu 26 kDa isozyme
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWolf, E. / Boergel, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Not funded Germany
CitationJournal: To Be Published
Title: A structural competition involving WDR5 times circadian oscillations
Authors: Wolf, E. / Boergel, A. / Rawleigh, A. / Conrady, M. / Hof, F. / Ricci, K. / Brown, S.
History
DepositionMar 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 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: Glutathione S-transferase class-mu 26 kDa isozyme,WD repeat domain 5
B: PER2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6947
Polymers64,1402
Non-polymers5535
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-20 kcal/mol
Surface area11800 Å2
Unit cell
Length a, b, c (Å)78.152, 78.152, 101.748
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Glutathione S-transferase class-mu 26 kDa isozyme,WD repeat domain 5 / GST 26 / Sj26 antigen / SjGST


Mass: 62673.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: WDR5 / Production host: Escherichia coli (E. coli)
References: UniProt: P08515, UniProt: A0A2K5BZZ6, glutathione transferase
#2: Protein/peptide PER2 peptide


Mass: 1466.656 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)

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Non-polymers , 4 types, 103 molecules

#3: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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

Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris pH 8.0, 50 mM sodium chloride, 13% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.85→78.15 Å / Num. obs: 27636 / % possible obs: 100 % / Redundancy: 14.2 % / CC1/2: 0.999 / Net I/σ(I): 18.3
Reflection shellResolution: 1.85→1.89 Å / Num. unique obs: 1653 / CC1/2: 0.955

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→39.11 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.383 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 1336 4.8 %RANDOM
Rwork0.16513 ---
obs0.16684 26251 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.936 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2---0.39 Å20 Å2
3---0.78 Å2
Refinement stepCycle: 1 / Resolution: 1.85→39.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2406 0 34 98 2538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132490
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172330
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.6293376
X-RAY DIFFRACTIONr_angle_other_deg1.4361.5865394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5485312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.36324.84597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40215412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.212153
X-RAY DIFFRACTIONr_chiral_restr0.080.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022769
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02529
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_it1.4761.8341254
X-RAY DIFFRACTIONr_mcbond_other1.4651.8321253
X-RAY DIFFRACTIONr_mcangle_it2.0542.741564
X-RAY DIFFRACTIONr_mcangle_other2.0592.7421565
X-RAY DIFFRACTIONr_scbond_it2.4082.0931235
X-RAY DIFFRACTIONr_scbond_other2.4072.0941236
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6233.0231813
X-RAY DIFFRACTIONr_long_range_B_refined4.43321.7462692
X-RAY DIFFRACTIONr_long_range_B_other4.43321.7582693
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 102 -
Rwork0.164 1900 -
obs--99.9 %

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