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

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Basic information

Entry
Database: PDB / ID: 2rhx
TitleCrystal structure of the 3-MBT repeats from human L3MBTL1 bound to dimethyl-lysine
ComponentsLethal(3)malignant brain tumor-like protein
KeywordsTRANSCRIPTION / Beta Barrel / dimethyl-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 / 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
N-DIMETHYL-LYSINE / TRIETHYLENE GLYCOL / Lethal(3)malignant brain tumor-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9066
Polymers39,1961
Non-polymers7115
Water5,513306
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.272, 93.104, 59.286
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#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: 39195.727 Da / Num. of mol.: 1 / Fragment: Repeates MBT-1, MBT-2, MBT-3; residues 197-526
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: L3MBTL, KIAA0681, L3MBT / Plasmid: pGex4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q9Y468

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Non-polymers , 5 types, 311 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MLY / N-DIMETHYL-LYSINE


Type: L-peptide linking / Mass: 174.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 3.04 Å3/Da / Density % sol: 59.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Crystals of the Kme2-L3MBTL1(197-526) complex were generated by pre-incubating L3MBTL1 (17MG/ML IN 50MM KCL, 25MM TRIS-HCL PH 8.0, 1MM DTT) with a five-fold molar excess of dimethyl-lysine ...Details: Crystals of the Kme2-L3MBTL1(197-526) complex were generated by pre-incubating L3MBTL1 (17MG/ML IN 50MM KCL, 25MM TRIS-HCL PH 8.0, 1MM DTT) with a five-fold molar excess of dimethyl-lysine amino acid. Drops were prepared by mixing equal volumes of the complex with reservoir solution (0.1 M bis-Tris, pH 6.5, 15% PEG MME 5000, 0.15 M ammonium sulfate, and 10 mM DTT)., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 28527 / Num. obs: 28356 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 20.3
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2800 / Rsym value: 0.572 / % possible all: 99.9

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Processing

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

1oz2


Resolution: 2.1→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
Rfree0.226 2158 -random
Rwork0.196 ---
all-28525 --
obs-26938 94.4 %-
Displacement parametersBiso mean: 38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2630 0 45 306 2981
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.43
X-RAY DIFFRACTIONc_bond_d0.006
LS refinement shellResolution: 2.1→2.17 Å
RfactorNum. reflection% reflection
Rfree0.2875 193 -
Rwork0.2573 --
obs-2342 83.9 %

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