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- PDB-2biv: Crystal structure of the wild-type MBT domains of Human SCML2 -

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Basic information

Entry
Database: PDB / ID: 2biv
TitleCrystal structure of the wild-type MBT domains of Human SCML2
ComponentsSEX COMB ON MIDLEG-LIKE PROTEIN 2
KeywordsTRANSCRIPTION / MALIGNANT BRAIN TUMOR / TRANSCRIPTION FACTOR
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 / SAM domain (Sterile alpha motif) / SH3 type barrels. - #140 / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Sex comb on midleg-like protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSantiveri, C.M. / Allen, M.D. / Sait, F. / 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
DepositionJan 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jan 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 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)82,92315
Polymers81,6083
Non-polymers1,31512
Water11,367631
1
A: SEX COMB ON MIDLEG-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5834
Polymers27,2031
Non-polymers3813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SEX COMB ON MIDLEG-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6065
Polymers27,2031
Non-polymers4044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SEX COMB ON MIDLEG-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7336
Polymers27,2031
Non-polymers5315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.020, 88.206, 186.988
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 PROTEIN


Mass: 27202.678 Da / Num. of mol.: 3 / Fragment: MBT DOMAIN, RESIDUES 1-243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSETA / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9UQR0
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 631 / 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: 2.02 Å3/Da / Density % sol: 39.17 %
Crystal growDetails: 0.14M SODIUM IODIDE, 20.5% PEG3350, 15MG/ML PROTEIN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→19.21 Å / Num. obs: 69311 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5.2 / % possible all: 87.8

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Processing

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

1oi1


Resolution: 1.7→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 3493 4.7 %RANDOM
Rwork0.1977 ---
obs0.1977 69250 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.3856 Å2 / ksol: 0.356413 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.621 Å20 Å20 Å2
2--0.372 Å20 Å2
3---1.249 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4838 0 12 631 5481
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.335
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_REP.PARAM

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