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- PDB-8ok1: WD repeat containing protein 5 (WDR5)- N225A mutant -

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Basic information

Entry
Database: PDB / ID: 8ok1
TitleWD repeat containing protein 5 (WDR5)- N225A mutant
ComponentsGlutathione S-transferase class-mu 26 kDa isozyme,WD repeat-containing protein 5
KeywordsGENE REGULATION / Scaffold protein / complex component / WD40 repeat
Function / homology
Function and homology information


Formation of WDR5-containing histone-modifying complexes / HATs acetylate histones / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Neddylation / MLL3/4 complex / Set1C/COMPASS complex / ATAC complex / NSL complex ...Formation of WDR5-containing histone-modifying complexes / HATs acetylate histones / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Neddylation / MLL3/4 complex / Set1C/COMPASS complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / histone methyltransferase complex / regulation of tubulin deacetylation / regulation of cell division / regulation of embryonic development / glutathione transferase / MLL1 complex / glutathione transferase activity / histone acetyltransferase complex / positive regulation of gluconeogenesis / methylated histone binding / glutathione metabolic process / transcription initiation-coupled chromatin remodeling / skeletal system development / gluconeogenesis / mitotic spindle / neuron projection development / histone binding / regulation of cell cycle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily ...Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-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
Glutathione S-transferase class-mu 26 kDa isozyme / WD repeat-containing protein 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase class-mu 26 kDa isozyme,WD repeat-containing protein 5


Theoretical massNumber of molelcules
Total (without water)62,6311
Polymers62,6311
Non-polymers00
Water4,414245
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11770 Å2
Unit cell
Length a, b, c (Å)78.498, 98.134, 80.055
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-632-

HOH

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Components

#1: Protein Glutathione S-transferase class-mu 26 kDa isozyme,WD repeat-containing protein 5 / GST 26 / Sj26 antigen / SjGST / BMP2-induced 3-kb gene protein / WD repeat-containing protein BIG-3


Mass: 62630.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Wdr5, Big, Big3 / Production host: Escherichia coli (E. coli)
References: UniProt: P08515, UniProt: P61965, glutathione transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5, 50 mM ammonium sulfate, 24% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.38→48.67 Å / Num. obs: 63526 / % possible obs: 99.3 % / Redundancy: 1.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.028 / Net I/σ(I): 13
Reflection shellResolution: 1.38→1.4 Å / Num. unique obs: 2949 / CC1/2: 0.573

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→48.67 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.254 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21774 3050 4.8 %RANDOM
Rwork0.19437 ---
obs0.19549 60006 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.859 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0.39 Å2
Refinement stepCycle: 1 / Resolution: 1.38→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 0 245 2572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132409
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172249
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.6223273
X-RAY DIFFRACTIONr_angle_other_deg1.4811.5865215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.635305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.33924.89494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55215409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.83152
X-RAY DIFFRACTIONr_chiral_restr0.090.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022707
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02525
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_it1.5571.6471217
X-RAY DIFFRACTIONr_mcbond_other1.5441.6441216
X-RAY DIFFRACTIONr_mcangle_it2.2062.4661523
X-RAY DIFFRACTIONr_mcangle_other2.212.4691524
X-RAY DIFFRACTIONr_scbond_it2.5681.921191
X-RAY DIFFRACTIONr_scbond_other2.5671.9221192
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9272.7581751
X-RAY DIFFRACTIONr_long_range_B_refined5.43920.4672679
X-RAY DIFFRACTIONr_long_range_B_other5.3720.0012632
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.381→1.417 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree1.164 219 -
Rwork1.254 4143 -
obs--94.35 %

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