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- PDB-1pk1: Hetero SAM domain structure of Ph and Scm. -

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Basic information

Entry
Database: PDB / ID: 1pk1
TitleHetero SAM domain structure of Ph and Scm.
Components
  • Polyhomeotic-proximal chromatin protein
  • Sex comb on midleg CG9495-PA
Keywordstranscription repression / Hetero SAM domain / polymers / transcriptional repression
Function / homology
Function and homology information


PRC1 complex binding / germarium-derived female germ-line cyst encapsulation / response to ecdysone / 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 / Transcriptional Regulation by E2F6 / Regulation of PTEN gene transcription / syncytial blastoderm mitotic cell cycle ...PRC1 complex binding / germarium-derived female germ-line cyst encapsulation / response to ecdysone / 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 / Transcriptional Regulation by E2F6 / Regulation of PTEN gene transcription / syncytial blastoderm mitotic cell cycle / follicle cell of egg chamber stalk formation / DNA topoisomerase binding / compound eye development / Oxidative Stress Induced Senescence / ventral cord development / PRC1 complex / polytene chromosome / negative regulation of growth / anterior/posterior axis specification / central nervous system neuron development / mitotic sister chromatid segregation / heterochromatin formation / axonogenesis / neurogenesis / histone binding / protein-folding chaperone binding / sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / regulation of transcription by RNA polymerase II / DNA binding / 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 / FCS-type zinc finger superfamily / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Mbt repeat ...Zinc finger, MYM-type / MYM-type Zinc finger with FCS sequence motif / : / SLED domain / SLED domain superfamily / SLED domain / FCS-type zinc finger superfamily / 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 (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
Polyhomeotic-proximal chromatin protein / Polycomb protein Scm
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 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 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyhomeotic-proximal chromatin protein
B: Sex comb on midleg CG9495-PA
C: Polyhomeotic-proximal chromatin protein
D: Sex comb on midleg CG9495-PA


Theoretical massNumber of molelcules
Total (without water)41,4594
Polymers41,4594
Non-polymers00
Water3,477193
1
A: Polyhomeotic-proximal chromatin protein
B: Sex comb on midleg CG9495-PA


Theoretical massNumber of molelcules
Total (without water)20,7292
Polymers20,7292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Polyhomeotic-proximal chromatin protein
D: Sex comb on midleg CG9495-PA


Theoretical massNumber of molelcules
Total (without water)20,7292
Polymers20,7292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.277, 46.866, 123.987
Angle α, β, γ (deg.)90.00, 90.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polyhomeotic-proximal chromatin protein


Mass: 10319.454 Da / Num. of mol.: 2 / Fragment: residue 1502-1577, Ph SAM domain / Mutation: L1565R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: PH-P / Plasmid: pET-3c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P39769
#2: Protein Sex comb on midleg CG9495-PA


Mass: 10409.959 Da / Num. of mol.: 2 / Fragment: residue 795-871, Scm SAM domain / Mutation: L841R, M846R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Sex Comb on Midleg / Plasmid: pET-3c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q9VHA0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 1000, ammonium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 20K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11281
21281
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X8C10.9795, 0.9797, 0.9720, 1.70
SYNCHROTRONALS 5.0.220.97
Detector
IDDetectorDate
1CCDFeb 11, 2002
2CCDFeb 1, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97971
30.9721
41.71
50.971
ReflectionResolution: 1.8→20 Å / Num. all: 28975 / Num. obs: 28975 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.7 Å2 / Rsym value: 0.029
Reflection shellResolution: 1.8→1.86 Å / % possible all: 76.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→19.56 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 881826.83 / Data cutoff high rms absF: 881826.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1420 4.9 %RANDOM
Rwork0.233 ---
obs0.233 28958 89.4 %-
all-28958 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.1946 Å2 / ksol: 0.470812 e/Å3
Displacement parametersBiso mean: 26.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å2-2.48 Å2
2--3.3 Å20 Å2
3----4.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å-0.01 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2150 0 0 193 2343
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_d18.5
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it2.472
X-RAY DIFFRACTIONc_scangle_it3.42.5
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 118 5.2 %
Rwork0.262 4056 -
obs-2336 73 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3&_1_TOPOLOGY_INFILE_3

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