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- PDB-1pk3: Scm SAM domain -

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Basic information

Entry
Database: PDB / ID: 1pk3
TitleScm SAM domain
ComponentsSex comb on midleg CG9495-PA
Keywordstranscription repression / SAM domain / polymer / transcriptional repression
Function / homology
Function and homology information


PRC1 complex binding / germarium-derived female germ-line cyst encapsulation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / follicle cell of egg chamber stalk formation / compound eye development / Oxidative Stress Induced Senescence ...PRC1 complex binding / germarium-derived female germ-line cyst encapsulation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / follicle cell of egg chamber stalk formation / compound eye development / Oxidative Stress Induced Senescence / ventral cord development / polytene chromosome / negative regulation of growth / anterior/posterior axis specification / heterochromatin formation / axonogenesis / neurogenesis / histone binding / sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / zinc ion binding / identical protein binding / nucleus
Similarity search - Function
Zinc finger, MYM-type / MYM-type Zinc finger with FCS sequence motif / : / SLED domain / SLED domain superfamily / SLED domain / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Mbt repeat / MBT repeat profile. ...Zinc finger, MYM-type / MYM-type Zinc finger with FCS sequence motif / : / SLED domain / SLED domain superfamily / SLED domain / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Polycomb protein Scm
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKim, C.A. / Sawaya, M.R. / Cascio, D. / Kim, W. / Bowie, J.U.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural organization of a Sex-comb-on-midleg/polyhomeotic copolymer.
Authors: Kim, C.A. / Sawaya, M.R. / Cascio, D. / Kim, W. / Bowie, J.U.
History
DepositionJun 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sex comb on midleg CG9495-PA
B: Sex comb on midleg CG9495-PA
C: Sex comb on midleg CG9495-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3866
Polymers31,1523
Non-polymers2343
Water2,630146
1
A: Sex comb on midleg CG9495-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4622
Polymers10,3841
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sex comb on midleg CG9495-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4622
Polymers10,3841
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sex comb on midleg CG9495-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4622
Polymers10,3841
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.150, 63.993, 103.638
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 CG9495-PA / Scm


Mass: 10383.961 Da / Num. of mol.: 3
Fragment: sequence database residue 795-871, SAM domain of Scm
Mutation: L841R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Scm / Plasmid: pET-3c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q9VHA0
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 318 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: ammonium acetate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 318K

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Data collection

DiffractionMean temperature: 148 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 25, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→80 Å / Num. all: 29232 / Num. obs: 29232 / % possible obs: 96.1 % / Biso Wilson estimate: 23.6 Å2 / Rsym value: 0.038
Reflection shellResolution: 1.85→1.92 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→19.84 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1155163.55 / Data cutoff high rms absF: 1155163.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1431 4.9 %RANDOM
Rwork0.215 ---
obs0.215 29172 96.1 %-
all-29172 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.591 Å2 / ksol: 0.420923 e/Å3
Displacement parametersBiso mean: 34.8 Å2
Baniso -1Baniso -2Baniso -3
1-16.42 Å20 Å20 Å2
2---7.21 Å20 Å2
3----9.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.85→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1768 0 0 158 1926
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it1.942
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.212.5
LS refinement shellResolution: 1.85→1.92 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 136 4.8 %
Rwork0.299 4708 -
obs-2791 99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMBME.TOP
X-RAY DIFFRACTION3BME.PARAM

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