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- PDB-6t1m: Crystal structure of MLLT1 (ENL) YEATS domain in complexed with b... -

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Basic information

Entry
Database: PDB / ID: 6t1m
TitleCrystal structure of MLLT1 (ENL) YEATS domain in complexed with benzimidazole-amide derivative 4
ComponentsProtein ENL
KeywordsTRANSCRIPTION / YEATS domain / ENL / MLLT1 / chemical probe / inhibitor / 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
YEATS domain / AF-9, ANC1 homology domain / : / ANC1 homology domain (AHD) / : / YEATS superfamily / YEATS family / YEATS domain profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-M8K / Protein ENL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChaikuad, A. / Heidenreich, D. / Moustakim, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Fedorov, O. / Brennan, P.E. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Acs Med.Chem.Lett. / Year: 2019
Title: Structural Insights into Interaction Mechanisms of Alternative Piperazine-urea YEATS Domain Binders in MLLT1.
Authors: Ni, X. / Heidenreich, D. / Christott, T. / Bennett, J. / Moustakim, M. / Brennan, P.E. / Fedorov, O. / Knapp, S. / Chaikuad, A.
History
DepositionOct 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 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)19,0199
Polymers18,2251
Non-polymers7948
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint18 kcal/mol
Surface area8720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.069, 49.069, 129.992
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: 18225.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT1, ENL, LTG19, YEATS1 / Plasmid: pNIC-CH / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2 / References: UniProt: Q03111
#2: Chemical ChemComp-M8K / 4-cyano-~{N}-[2-(piperidin-1-ylmethyl)-1~{H}-benzimidazol-5-yl]benzamide


Mass: 359.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.2M sodium chloride, 0.1M bis-tris pH 5.5

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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: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→49.07 Å / Num. obs: 14360 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 35.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.029 / Rrim(I) all: 0.094 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.85-1.9110.40.82.113680.930.2670.875100
7.17-49.078.30.0743220.9980.0260.07999.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HQ0

6hq0


Resolution: 1.85→45.91 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.929 / SU B: 15.067 / SU ML: 0.19 / SU R Cruickshank DPI: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.159
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2745 690 4.8 %RANDOM
Rwork0.2152 ---
obs0.2181 13605 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 109.51 Å2 / Biso mean: 50.56 Å2 / Biso min: 30.64 Å2
Baniso -1Baniso -2Baniso -3
1--4.07 Å20 Å20 Å2
2---4.07 Å20 Å2
3---8.14 Å2
Refinement stepCycle: final / Resolution: 1.85→45.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1177 0 55 48 1280
Biso mean--61.13 50.7 -
Num. residues----142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131272
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171184
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.6651707
X-RAY DIFFRACTIONr_angle_other_deg1.1191.6012745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7555143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.10520.94674
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50515213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1731511
X-RAY DIFFRACTIONr_chiral_restr0.060.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021483
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02290
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 48 -
Rwork0.364 971 -
all-1019 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -0.6396 Å / Origin y: -3.9279 Å / Origin z: 12.6521 Å
111213212223313233
T0.0229 Å2-0.025 Å20.0011 Å2-0.0391 Å2-0.0132 Å2--0.0331 Å2
L2.1432 °2-0.9605 °20.0065 °2-3.1605 °2-0.488 °2--0.1663 °2
S0.1395 Å °-0.1521 Å °-0.0533 Å °-0.0593 Å °-0.1055 Å °0.1335 Å °-0.0333 Å °0.0672 Å °-0.0339 Å °

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