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- PDB-2vyt: The MBT repeats of human SCML2 bind to peptides containing mono m... -

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Basic information

Entry
Database: PDB / ID: 2vyt
TitleThe MBT repeats of human SCML2 bind to peptides containing mono methylated lysine.
ComponentsSEX COMB ON MIDLEG-LIKE PROTEIN 2
KeywordsTRANSCRIPTION / MONO METHYLATED PEPTIDES / MBT REPEATS / PHOSPHOPROTEIN / ALTERNATIVE SPLICING / TRANSCRIPTION REGULATION / NUCLEUS / REPRESSOR / CHROMATIN / HUMAN SCML2
Function / homology
Function and homology information


PcG protein complex / anatomical structure morphogenesis / histone binding / negative regulation of DNA-templated transcription / chromatin binding / nucleus
Similarity search - Function
Polycomb group protein, RNA binding region / RNA binding Region / : / SLED domain / SLED domain superfamily / SLED domain / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat ...Polycomb group protein, RNA binding region / RNA binding Region / : / SLED domain / SLED domain superfamily / SLED domain / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat / SH3 type barrels. - #140 / SAM domain (Sterile alpha motif) / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
N-METHYL-LYSINE / TRIETHYLENE GLYCOL / Sex comb on midleg-like protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSantiveri, C.M. / Lechtenberg, B.C. / Allen, M.D. / Sathyamurthy, A. / Jaulent, A.M. / Freund, S.M.V. / Bycroft, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The Malignant Brain Tumor Repeats of Human Scml2 Bind to Peptides Containing Monomethylated Lysine.
Authors: Santiveri, C.M. / Lechtenberg, B.C. / Allen, M.D. / Sathyamurthy, A. / Jaulent, A.M. / Freund, S.M.V. / Bycroft, M.
History
DepositionJul 28, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SEX COMB ON MIDLEG-LIKE PROTEIN 2
B: SEX COMB ON MIDLEG-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7725
Polymers49,3022
Non-polymers4713
Water3,369187
1
A: SEX COMB ON MIDLEG-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8112
Polymers24,6511
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SEX COMB ON MIDLEG-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9613
Polymers24,6511
Non-polymers3102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.530, 99.210, 131.277
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SEX COMB ON MIDLEG-LIKE PROTEIN 2 / SCML2 / HUMAN MBT


Mass: 24650.818 Da / Num. of mol.: 2 / Fragment: MBT REPEATS, RESIDUES 24-243 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9UQR0
#2: Chemical ChemComp-MLZ / N-METHYL-LYSINE


Type: L-peptide linking / Mass: 160.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16N2O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 147 TO GLU ENGINEERED RESIDUE IN CHAIN B, LYS 147 TO GLU
Sequence detailsMUTATION K147E

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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: 2.53 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 9.5
Details: 0.1M CHES, PH 9.5 40% PEG 600 5MM MONOMETHYLATD LYSINE 10MM MBT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.954
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.9→30.4 Å / Num. obs: 40544 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.2
Reflection shellHighest resolution: 1.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OI1

1oi1


Resolution: 1.9→30 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 2005 4.9 %1
Rwork0.2167 ---
obs0.2167 40481 99.6 %-
Solvent computationBsol: 63.7487 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 31.26 Å2
Baniso -1Baniso -2Baniso -3
1-3.495 Å20 Å20 Å2
2---4.443 Å20 Å2
3---0.949 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3123 0 32 187 3342
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.444
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER.PARAM
X-RAY DIFFRACTION4NHE.PAR
X-RAY DIFFRACTION5PEG.PAR

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