+Open data
-Basic information
Entry | Database: PDB / ID: 1kw4 | ||||||
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Title | Polyhomeotic SAM domain structure | ||||||
Components | Polyhomeotic | ||||||
Keywords | DNA 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 | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å | ||||||
Authors | Kim, C.A. / Gingery, M. / M Pilpa, R. / Bowie, J.U. | ||||||
Citation | Journal: 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 |
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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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kw4.cif.gz | 23.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kw4.ent.gz | 17 KB | Display | PDB format |
PDBx/mmJSON format | 1kw4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/1kw4 ftp://data.pdbj.org/pub/pdb/validation_reports/kw/1kw4 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.27 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.969575, 0.97855, 0.979224 | ||||||||||||
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 13, 2001 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 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 shell | Highest 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 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 68.2429 Å2 / ksol: 0.407488 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→1.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.81 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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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
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LS refinement shell | *PLUS Rfactor Rfree: 0.261 / Rfactor Rwork: 0.244 / Rfactor obs: 0.244 |