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- PDB-5r69: XChem group deposition -- Crystal Structure of human YEATS4 in co... -

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Basic information

Entry
Database: PDB / ID: 5r69
TitleXChem group deposition -- Crystal Structure of human YEATS4 in complex with XS038644e
ComponentsYEATS domain-containing protein 4
KeywordsTRANSCRIPTION / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / HISTONE READER / YEATS DOMAIN
Function / homology
Function and homology information


histone H3K18ac reader activity / histone H3K27ac reader activity / Activation of the TFAP2 (AP-2) family of transcription factors / regulation of double-strand break repair / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / structural constituent of cytoskeleton / nuclear matrix / nucleosome / mitotic cell cycle ...histone H3K18ac reader activity / histone H3K27ac reader activity / Activation of the TFAP2 (AP-2) family of transcription factors / regulation of double-strand break repair / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / structural constituent of cytoskeleton / nuclear matrix / nucleosome / mitotic cell cycle / HATs acetylate histones / nuclear membrane / regulation of apoptotic process / histone binding / regulation of cell cycle / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleoplasm / nucleus
Similarity search - Function
YEATS / : / YEATS superfamily / YEATS family / YEATS domain profile.
Similarity search - Domain/homology
Chem-ZHA / YEATS domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.83 Å
AuthorsRaux, B. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Huber, K.V.M.
CitationJournal: To Be Published
Title: XChem group deposition
Authors: Raux, B. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Huber, K.V.M.
History
DepositionFeb 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: YEATS domain-containing protein 4
A: YEATS domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2067
Polymers42,6132
Non-polymers5935
Water2,288127
1
B: YEATS domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5723
Polymers21,3061
Non-polymers2652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: YEATS domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6344
Polymers21,3061
Non-polymers3273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.600, 47.440, 58.450
Angle α, β, γ (deg.)67.580, 68.560, 69.020
Int Tables number1
Space group name H-MP1

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Components

#1: Protein YEATS domain-containing protein 4 / Glioma-amplified sequence 41 / Gas41 / NuMA-binding protein 1 / NuBI1


Mass: 21306.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YEATS4, GAS41 / Production host: escherichia coli (E. coli) / References: UniProt: O95619
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZHA / ~{N}-(5-oxidanylidene-7,8-dihydro-6~{H}-naphthalen-2-yl)ethanamide


Mass: 203.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.19 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M tris pH 7.5, 0.15M lithium sulfate, 40% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.83→42.41 Å / Num. obs: 34543 / % possible obs: 96.1 % / Redundancy: 1.8 % / CC1/2: 0.956 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.138 / Rrim(I) all: 0.195 / Net I/σ(I): 7.4 / Num. measured all: 62153 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.83-1.881.80.781469325430.5670.7811.1041.195
8.18-42.4120.0597873990.9750.0590.08323.898

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0257refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5VNA

5vna


Resolution: 1.83→42.45 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.357 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 1701 4.9 %RANDOM
Rwork0.2286 ---
obs0.2296 32842 96.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.5 Å2 / Biso mean: 25.148 Å2 / Biso min: 13.21 Å2
Baniso -1Baniso -2Baniso -3
1-2.49 Å21.11 Å21.12 Å2
2--0.48 Å21.11 Å2
3----0.75 Å2
Refinement stepCycle: final / Resolution: 1.83→42.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2191 0 42 127 2360
Biso mean--34.05 33.71 -
Num. residues----265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132307
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172126
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.6793127
X-RAY DIFFRACTIONr_angle_other_deg1.2831.5884932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0335264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.47322.87115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71315386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.928159
X-RAY DIFFRACTIONr_chiral_restr0.0730.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022594
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02493
X-RAY DIFFRACTIONr_mcbond_it2.0612.5271065
X-RAY DIFFRACTIONr_mcbond_other2.062.5281066
X-RAY DIFFRACTIONr_mcangle_it3.1153.7761328
LS refinement shellResolution: 1.83→1.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 112 -
Rwork0.337 2427 -
all-2539 -
obs--94.99 %

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