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- PDB-1kw4: Polyhomeotic SAM domain structure -

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Basic information

Entry
Database: PDB / ID: 1kw4
TitlePolyhomeotic SAM domain structure
ComponentsPolyhomeotic
KeywordsDNA BINDING PROTEIN / SAM domain / Polycomb Group / polymer
Function / homology
Function and homology information


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 ...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 / PRC1 complex / polytene chromosome / anterior/posterior axis specification / central nervous system neuron development / mitotic sister chromatid segregation / heterochromatin formation / 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 / nucleus
Similarity search - Function
FCS-type zinc finger superfamily / Zinc finger, FCS-type / Zinc finger FCS-type profile. / 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 ...FCS-type zinc finger superfamily / Zinc finger, FCS-type / Zinc finger FCS-type profile. / 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
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsKim, C.A. / Gingery, M. / M Pilpa, R. / Bowie, J.U.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: The SAM domain of polyhomeotic forms a helical polymer.
Authors: Kim, C.A. / Gingery, M. / Pilpa, R.M. / Bowie, J.U.
History
DepositionJan 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_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
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE RELEVANT BIOLOGICAL UNIT MAY BE THE 65 POLYMER. HOWEVER, THE EXACT STOICHIOMETRY OF THE POLYMER CANNOT BE STATED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyhomeotic


Theoretical massNumber of molelcules
Total (without water)10,3191
Polymers10,3191
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.836, 59.836, 44.896
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Polyhomeotic


Mass: 10319.455 Da / Num. of mol.: 1 / Fragment: SAM domain / Mutation: L51R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: P39769
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Li2SO4, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
116-20 mg/mlprotein1drop
250 mMsodium citrate1reservoirpH4.0
31.9 M1reservoirLi2SO4

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.969575, 0.97855, 0.979224
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 13, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9695751
20.978551
30.9792241
ReflectionResolution: 1.75→20 Å / Num. obs: 17395 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.5 Å2
Reflection shellHighest resolution: 1.75 Å / % possible all: 97
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 99.1 % / Num. measured all: 224372 / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
Lowest resolution: 1.81 Å / % possible obs: 100 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 12

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.75→1.81 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1256045.07 / Data cutoff high rms absF: 1256045.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 488 5.3 %RANDOM
Rwork0.22 ---
obs0.22 9145 98 %-
all-9335 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.2429 Å2 / ksol: 0.407488 e/Å3
Displacement parametersBiso mean: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.82 Å20.2 Å20 Å2
2---2.82 Å20 Å2
3---5.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.75→1.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms551 0 0 56 607
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.5
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_mcangle_it2.432
X-RAY DIFFRACTIONc_scbond_it2.672
X-RAY DIFFRACTIONc_scangle_it4.22.5
LS refinement shellResolution: 1.75→1.81 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.261 62 4.4 %
Rwork0.244 1357 -
obs--91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.22 / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0056
X-RAY DIFFRACTIONc_angle_deg1.16
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94
LS refinement shell
*PLUS
Rfactor Rfree: 0.261 / Rfactor Rwork: 0.244 / Rfactor obs: 0.244

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