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- PDB-5r68: XChem group deposition -- Crystal Structure of human YEATS4 in co... -

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Basic information

Entry
Database: PDB / ID: 5r68
TitleXChem group deposition -- Crystal Structure of human YEATS4 in complex with FM000199e
ComponentsYEATS domain-containing protein 4
KeywordsTRANSCRIPTION / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / HISTONE READER / YEATS DOMAIN
Function / homology
Function and homology information


modification-dependent protein binding / regulation of double-strand break repair / Activation of the TFAP2 (AP-2) family of transcription factors / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / lysine-acetylated histone binding / structural constituent of cytoskeleton / nuclear matrix / nucleosome / mitotic cell cycle ...modification-dependent protein binding / regulation of double-strand break repair / Activation of the TFAP2 (AP-2) family of transcription factors / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / lysine-acetylated histone binding / structural constituent of cytoskeleton / nuclear matrix / nucleosome / mitotic cell cycle / HATs acetylate histones / histone binding / regulation of apoptotic process / nuclear membrane / 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
(1-methylbenzotriazol-5-yl)methanol / YEATS domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.64 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)43,2509
Polymers42,6132
Non-polymers6377
Water2,180121
1
B: YEATS domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5944
Polymers21,3061
Non-polymers2873
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)21,6565
Polymers21,3061
Non-polymers3494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.880, 46.810, 58.340
Angle α, β, γ (deg.)67.390, 68.460, 69.570
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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-RYD / (1-methylbenzotriazol-5-yl)methanol


Mass: 163.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H9N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.4 Å3/Da / Density % sol: 48.67 % / 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: 1.64→41.93 Å / Num. obs: 46555 / % possible obs: 96.1 % / Redundancy: 1.8 % / CC1/2: 0.98 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.08 / Rrim(I) all: 0.113 / Net I/σ(I): 8.5 / Num. measured all: 82967 / 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
1.64-1.681.80.67611534100.6140.670.9481.195.2
7.33-41.9320.03210295210.9930.0320.04527.597.2

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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: 1.64→41.96 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.096 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 2329 5 %RANDOM
Rwork0.2197 ---
obs0.2212 44226 96.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.2 Å2 / Biso mean: 24.21 Å2 / Biso min: 12.61 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å20.92 Å20.8 Å2
2--0.64 Å20.34 Å2
3----0.95 Å2
Refinement stepCycle: final / Resolution: 1.64→41.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2165 0 44 121 2330
Biso mean--34.05 33.33 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132289
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172131
X-RAY DIFFRACTIONr_angle_refined_deg1.681.6793095
X-RAY DIFFRACTIONr_angle_other_deg1.3471.5844936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5275261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6422.522115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25515391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8261510
X-RAY DIFFRACTIONr_chiral_restr0.080.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022581
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02493
X-RAY DIFFRACTIONr_mcbond_it2.3562.3781052
X-RAY DIFFRACTIONr_mcbond_other2.3552.3781053
X-RAY DIFFRACTIONr_mcangle_it3.3353.551309
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 177 -
Rwork0.35 3229 -
all-3406 -
obs--95.11 %

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