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- PDB-6hq0: Crystal structure of ENL (MLLT1), apo form -

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Basic information

Entry
Database: PDB / ID: 6hq0
TitleCrystal structure of ENL (MLLT1), apo form
ComponentsProtein ENL
KeywordsTRANSCRIPTION / YEATS domain / inhibitor complex / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsHeidenreich, D. / Chaikuad, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2018
Title: Structure-Based Approach toward Identification of Inhibitory Fragments for Eleven-Nineteen-Leukemia Protein (ENL).
Authors: Heidenreich, D. / Moustakim, M. / Schmidt, J. / Merk, D. / Brennan, P.E. / Fedorov, O. / Chaikuad, A. / Knapp, S.
History
DepositionSep 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 24, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 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

Downloads & links

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Assembly

Deposited unit
A: Protein ENL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6226
Polymers18,3121
Non-polymers3105
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint15 kcal/mol
Surface area8370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.419, 49.419, 128.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 18312.080 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): Rosetta / References: UniProt: Q03111
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 82 / 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

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 2000MME, 0.1M KBr

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.81→46.12 Å / Num. obs: 15436 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 27.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.028 / Net I/σ(I): 14.3
Reflection shellResolution: 1.81→1.84 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 895 / CC1/2: 0.768 / Rpim(I) all: 0.286 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5j9s

5j9s


Resolution: 1.81→39.18 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.955 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.129 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23661 757 4.9 %RANDOM
Rwork0.1915 ---
obs0.19369 14612 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.092 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å20 Å20 Å2
2---1.43 Å20 Å2
3---2.86 Å2
Refinement stepCycle: 1 / Resolution: 1.81→39.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1155 0 20 82 1257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131234
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171158
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.671666
X-RAY DIFFRACTIONr_angle_other_deg1.2961.5742691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5285146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.53521.11172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93115213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9191510
X-RAY DIFFRACTIONr_chiral_restr0.0720.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021350
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02280
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_it2.0242.356563
X-RAY DIFFRACTIONr_mcbond_other2.0262.353562
X-RAY DIFFRACTIONr_mcangle_it3.2173.519704
X-RAY DIFFRACTIONr_mcangle_other3.2153.522705
X-RAY DIFFRACTIONr_scbond_it2.8982.801671
X-RAY DIFFRACTIONr_scbond_other2.8962.804672
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5164.028959
X-RAY DIFFRACTIONr_long_range_B_refined7.35928.4261306
X-RAY DIFFRACTIONr_long_range_B_other7.35828.4221306
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.805→1.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 63 -
Rwork0.229 1032 -
obs--99.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7942-0.9240.39692.3112-0.35080.2179-0.0139-0.12750.01230.09280.0179-0.0371-0.0322-0.0729-0.00410.11820.00230.01450.0796-0.03060.026-2.70110.164514.2138
20.581-0.67320.1971.9926-0.10250.09720.06840.01340.072-0.1386-0.0771-0.171-0.01790.0190.00870.10890.00270.01970.083-0.01420.03282.2317-1.05468.0649
32.6131-2.192-0.58883.4614-1.92193.95960.0996-0.1195-0.3863-0.0859-0.07750.27550.0970.2687-0.02210.0651-0.0149-0.10750.02630.03850.19852.9567-22.832113.2964
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 91
2X-RAY DIFFRACTION2A92 - 121
3X-RAY DIFFRACTION3A122 - 143

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