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- PDB-2rhy: Crystal structure of the 3-MBT repeats from human L3MBTL1 bound t... -

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Basic information

Entry
Database: PDB / ID: 2rhy
TitleCrystal structure of the 3-MBT repeats from human L3MBTL1 bound to monomethyl-lysine
ComponentsLethal(3)malignant brain tumor-like protein
KeywordsTRANSCRIPTION / Beta barrel / monomethyl-lysine / Alternative splicing / Chromatin regulator / DNA-binding / Metal-binding / Nucleus / Repressor / Transcription regulation / Zinc / Zinc-finger
Function / homology
Function and homology information


SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / heterochromatin formation / nucleosome binding / condensed chromosome / methylated histone binding / Regulation of TP53 Activity through Methylation ...SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / heterochromatin formation / nucleosome binding / condensed chromosome / methylated histone binding / Regulation of TP53 Activity through Methylation / 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 / mbt repeat ...: / : / 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
N-METHYL-LYSINE / DI(HYDROXYETHYL)ETHER / Lethal(3)malignant brain tumor-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Molrep / Resolution: 1.9 Å
AuthorsLi, H. / Patel, D.J.
CitationJournal: Mol.Cell / Year: 2007
Title: Structural Basis for Lower Lysine Methylation State-Specific Readout by MBT Repeats of L3MBTL1 and an Engineered PHD Finger.
Authors: Li, H. / Fischle, W. / Wang, W. / Duncan, E.M. / Liang, L. / Murakami-Ishibe, S. / Allis, C.D. / Patel, D.J.
History
DepositionOct 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9603
Polymers36,6941
Non-polymers2662
Water8,269459
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.460, 92.607, 58.674
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Lethal(3)malignant brain tumor-like protein / L3 / mbt-like / L3 / mbt protein homolog / H-l3 / mbt protein / H-L3 / MBT / L3MBTL1


Mass: 36693.957 Da / Num. of mol.: 1 / Fragment: Repeates MBT-1, MBT-2, MBT-3; residues 206-519
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: L3MBTL, KIAA0681, L3MBT / Plasmid: pGex6p / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q9Y468
#2: Chemical ChemComp-MLZ / N-METHYL-LYSINE


Type: L-peptide linking / Mass: 160.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16N2O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 3.16 Å3/Da / Density % sol: 61.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Crystals was generated by pre-incubating the L3MBTL1 (12MG/ML IN 50MM KCL, 25MM TRIS-HCL PH 8.0, 1MM DTT) with a five-fold molar excess of monomethyl-lysine amino acid. Drops were prepared ...Details: Crystals was generated by pre-incubating the L3MBTL1 (12MG/ML IN 50MM KCL, 25MM TRIS-HCL PH 8.0, 1MM DTT) with a five-fold molar excess of monomethyl-lysine amino acid. Drops were prepared by mixing equal volumes of the complex with reservoir solution (7.5% PEG10K, 0.1 M Tris-maleate pH 6.5, 0.1 M ammonium sulfate), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 15, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 37497 / Num. obs: 37422 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 24.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3665 / Rsym value: 0.485 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: Molrep
Starting model: 1OZ2

1oz2


Resolution: 1.9→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2121 -RANDOM
Rwork0.21 ---
all-37377 --
obs-35569 95.2 %-
Displacement parametersBiso mean: 32.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2572 0 11 466 3049
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONc_bond_d0.006
LS refinement shellResolution: 1.9→1.97 Å
RfactorNum. reflection% reflection
Rfree0.293 198 -
Rwork0.289 --
obs-3220 87.6 %

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