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- PDB-1oi1: Crystal Structure of the MBT domains of Human SCML2 -

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Basic information

Entry
Database: PDB / ID: 1oi1
TitleCrystal Structure of the MBT domains of Human SCML2
ComponentsSCML2 PROTEIN
KeywordsMBT / 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 / 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
DI(HYDROXYETHYL)ETHER / Sex comb on midleg-like protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 1.78 Å
AuthorsSathyamurthy, A. / Allen, M.D. / Murzin, A.G. / Bycroft, M.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of the Malignant Brain Tumor (Mbt) Repeats in Sex Comb on Midleg-Like 2 (Scml2).
Authors: Sathyamurthy, A. / Allen, M.D. / Murzin, A.G. / Bycroft, M.
History
DepositionJun 4, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SCML2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7572
Polymers24,6511
Non-polymers1061
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)118.762, 47.696, 41.493
Angle α, β, γ (deg.)90.00, 100.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SCML2 PROTEIN


Mass: 24650.818 Da / Num. of mol.: 1 / Fragment: RESIDUES 24-243 MBT DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: CDNA SUBCLONED / Plasmid: PRSETA / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9UQR0
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION LYS147GLU THIS MUTATION IS NEEDED FOR STABILITY
Sequence detailsN-TERMINAL G NEEDED FOR CLONING

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47 %
Crystal growpH: 8
Details: 0.1 M TRIS, PH 8.0, 50MM MAGNESIUM CHLORIDE, 15.6% PEG4000 PEG200 (20%) - AS CRYOPROTECTANT
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
210 mMTris1droppH7.5
35 mMdithiothreitol1drop
4100 mMTris1reservoirpH8.0
515.6 %PEG40001reservoir
650 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5417
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.78→31.01 Å / Num. obs: 21472 / % possible obs: 97.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 19.8
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 6.2 / % possible all: 94.7
Reflection
*PLUS
Highest resolution: 1.78 Å / Lowest resolution: 31.01 Å / Redundancy: 5.5 % / Num. measured all: 117212 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 94.7 % / Redundancy: 5.2 % / Num. unique obs: 3022 / Num. measured obs: 15686 / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 6.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVE/RESOLVEphasing
CNSphasing
CNS1.1refinement
RefinementMethod to determine structure: MIRAS / Resolution: 1.78→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1077 5 %RANDOM
Rwork0.171 ---
obs0.171 20369 97.13 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--1.748 Å20 Å2
3----2.058 Å2
Refinement stepCycle: LAST / Resolution: 1.78→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 7 308 1945
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0044
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_deg1.304
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
LS refinement shellResolution: 1.78→1.81 Å / Total num. of bins used: 21 /
RfactorNum. reflection
Rfree0.26 56
Rwork0.209 915
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PROTEIN_BREAK.TOP
Refinement
*PLUS
Num. reflection all: 21446
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3

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