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- PDB-7b0t: Crystal structure of MLLT1 YEATS domain T3 mutant in complex with... -

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Basic information

Entry
Database: PDB / ID: 7b0t
TitleCrystal structure of MLLT1 YEATS domain T3 mutant in complex with benzimidazole-amide based compound 1
ComponentsProtein ENL
KeywordsTRANSCRIPTION / T3 mutant / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / : / RNA Polymerase II Pre-transcription Events / transcription elongation factor complex / fibrillar center / chromatin binding / positive regulation of DNA-templated transcription / nucleoplasm / cytosol
Similarity search - Function
AF-9, ANC1 homology domain / : / ANC1 homology domain (AHD) / : / YEATS superfamily / YEATS family / YEATS domain profile.
Similarity search - Domain/homology
Chem-GKT / Protein ENL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsNi, X. / Chaikuad, A. / Brennan, P.E. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Structure and Inhibitor Binding Characterization of Oncogenic MLLT1 Mutants.
Authors: Ni, X. / Londregan, A.T. / Owen, D.R. / Knapp, S. / Chaikuad, A.
History
DepositionNov 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Protein ENL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8317
Polymers18,0461
Non-polymers7856
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint11 kcal/mol
Surface area7850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.739, 48.739, 131.995
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein ENL / YEATS domain-containing protein 1


Mass: 18045.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT1, ENL, LTG19, YEATS1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q03111
#2: Chemical ChemComp-GKT / 3-iodanyl-4-methyl-~{N}-[2-(piperidin-1-ylmethyl)-3~{H}-benzimidazol-5-yl]benzamide


Mass: 474.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23IN4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 28% PEG 3350, 0.2M NaOAc, 0.1M Bis-Tris, pH6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→48.74 Å / Num. obs: 10697 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.031 / Rrim(I) all: 0.099 / Net I/σ(I): 11.5 / Num. measured all: 103164 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) all% possible allRrim(I) all
2.05-2.1110.11.1698040.8580.378100
8.94-48.747.50.0551820.9980.01999.90.059

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6t1j

6t1j


Resolution: 2.05→45.72 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 17.371 / SU ML: 0.212 / SU R Cruickshank DPI: 0.2123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2756 496 4.7 %RANDOM
Rwork0.218 ---
obs0.2208 10142 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.93 Å2 / Biso mean: 56.281 Å2 / Biso min: 35.43 Å2
Baniso -1Baniso -2Baniso -3
1--2.7 Å20 Å20 Å2
2---2.7 Å20 Å2
3---5.41 Å2
Refinement stepCycle: final / Resolution: 2.05→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1123 0 47 13 1183
Biso mean--62.81 50.55 -
Num. residues----138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131201
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171133
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.6621616
X-RAY DIFFRACTIONr_angle_other_deg1.1771.6082598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8615137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.47720.30865
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.09115194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9871510
X-RAY DIFFRACTIONr_chiral_restr0.0640.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021411
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02297
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 40 -
Rwork0.308 725 -
all-765 -
obs--99.87 %
Refinement TLS params.Method: refined / Origin x: -0.8921 Å / Origin y: -4.0944 Å / Origin z: 12.9729 Å
111213212223313233
T0.0159 Å2-0.0132 Å20.0001 Å2-0.0194 Å2-0.0165 Å2--0.1513 Å2
L3.6929 °2-2.5145 °2-0.4478 °2-5.8809 °2-0.7502 °2--1.3182 °2
S0.1301 Å °-0.2367 Å °-0.0132 Å °0.0605 Å °0.0783 Å °0.0381 Å °-0.1182 Å °0.0921 Å °-0.2084 Å °

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