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- PDB-3uwn: The 3-MBT repeat domain of L3MBTL1 in complex with a methyl-lysin... -

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Basic information

Entry
Database: PDB / ID: 3uwn
TitleThe 3-MBT repeat domain of L3MBTL1 in complex with a methyl-lysine mimic
ComponentsLethal(3)malignant brain tumor-like protein 1
KeywordsTRANSCRIPTION / STRUCTURAL GENOMICS CONSORTIUM / SGC / MBT REPEAT / histone modification
Function / homology
Function and homology information


SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / nucleosome binding / condensed chromosome / methylated histone binding / Regulation of TP53 Activity through Methylation / heterochromatin formation ...SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / nucleosome binding / condensed chromosome / methylated histone binding / Regulation of TP53 Activity through Methylation / heterochromatin formation / chromatin organization / histone binding / regulation of cell cycle / negative regulation of DNA-templated transcription / chromatin binding / chromatin / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / : / Zinc finger, C2H2C-type superfamily / Zinc finger, C2HC type / Zinc finger, C2H2C-type / Zinc finger CCHHC-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / : ...: / : / Zinc finger, C2H2C-type superfamily / Zinc finger, C2HC type / Zinc finger, C2H2C-type / Zinc finger CCHHC-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / : / mbt repeat / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Chem-UWN / Lethal(3)malignant brain tumor-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsZhong, N. / Tempel, W. / Wernimont, A.K. / Graslund, S. / Ingerman, L.A. / Korboukh, V. / Kireev, D.B. / Gao, C. / Frye, S.V. / Arrowsmith, C.H. ...Zhong, N. / Tempel, W. / Wernimont, A.K. / Graslund, S. / Ingerman, L.A. / Korboukh, V. / Kireev, D.B. / Gao, C. / Frye, S.V. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Brown, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The 3-MBT repeat domain of L3MBTL1 in complex with a methyl-lysine mimic
Authors: Zhong, N. / Tempel, W. / Wernimont, A.K. / Graslund, S. / Ingerman, L.A. / Korboukh, V. / Kireev, D.B. / Gao, C. / Frye, S.V. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / ...Authors: Zhong, N. / Tempel, W. / Wernimont, A.K. / Graslund, S. / Ingerman, L.A. / Korboukh, V. / Kireev, D.B. / Gao, C. / Frye, S.V. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Brown, P.J. / Structural Genomics Consortium (SGC)
History
DepositionDec 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.type / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lethal(3)malignant brain tumor-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,28116
Polymers37,7511
Non-polymers53015
Water1,76598
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.774, 94.530, 58.955
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

#1: Protein Lethal(3)malignant brain tumor-like protein 1 / H-l(3)mbt / H-l(3)mbt protein / L(3)mbt-like / L(3)mbt protein homolog / L3MBTL1


Mass: 37751.211 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 200-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: L3MBTL1, KIAA0681, L3MBT, L3MBTL / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q9Y468
#2: Chemical ChemComp-UWN / [2-(phenylamino)benzene-1,4-diyl]bis{[4-(pyrrolidin-1-yl)piperidin-1-yl]methanone}


Mass: 529.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H43N5O2
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 14 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.3 Å3/Da / Density % sol: 62.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG-3350, 0.1 M ammonium sulfate, 0.1 M bis-tris. Crystal was soaked for 2 days in a 0.001 M solution of the ligand., pH 5.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
a2001001
11
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Sep 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→29.58 Å / Num. obs: 26687 / % possible obs: 99.75 % / Redundancy: 6.49 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 15.0444
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allDiffraction-ID% possible all
2.15-2.275.490.9209413815199.29
2.27-2.45.90.7212493601199.75
2.4-2.576.360.48219343448199.87
2.57-2.786.730.31214333185199.85
2.78-3.046.960.18206472966199.96
3.04-3.47.030.091884726821100
3.4-3.9370.06168582409199.96
3.93-4.816.990.04142072033199.88
4.81-6.86.860.04110801614199.86
6.8-29.586.30.025881934198.32

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.20data scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1oyx

1oyx


Resolution: 2.15→29.58 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.899 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.229 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY Ligand geometry restraints were prepared on the PRODRG server. The program COOT and the MOLPROBITY server ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY Ligand geometry restraints were prepared on the PRODRG server. The program COOT and the MOLPROBITY server were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1348 5.1 %RANDOM
Rwork0.2309 ---
obs0.2327 26655 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.27 Å2 / Biso mean: 30.8562 Å2 / Biso min: 14.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å20 Å20 Å2
2--1.3 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2532 0 42 98 2672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022707
X-RAY DIFFRACTIONr_bond_other_d0.0020.021817
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9333716
X-RAY DIFFRACTIONr_angle_other_deg0.8553.0064413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.485328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.02923.672128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87515373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5041511
X-RAY DIFFRACTIONr_chiral_restr0.080.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213053
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02584
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 92 -
Rwork0.307 1673 -
all-1765 -
obs--98.66 %

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