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Yorodumi- PDB-1fjl: HOMEODOMAIN FROM THE DROSOPHILA PAIRED PROTEIN BOUND TO A DNA OLI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fjl | ||||||
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Title | HOMEODOMAIN FROM THE DROSOPHILA PAIRED PROTEIN BOUND TO A DNA OLIGONUCLEOTIDE | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / DNA-BINDING PROTEIN / DNA / PAIRED BOX / TRANSCRIPTION REGULATION / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information periodic partitioning by pair rule gene / HATs acetylate histones / anatomical structure development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Wilson, D.S. / Guenther, B. / Desplan, C. / Kuriyan, J. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1995 Title: High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA. Authors: Wilson, D.S. / Guenther, B. / Desplan, C. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fjl.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fjl.ent.gz | 61.9 KB | Display | PDB format |
PDBx/mmJSON format | 1fjl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/1fjl ftp://data.pdbj.org/pub/pdb/validation_reports/fj/1fjl | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | A COMPLEX OF TWO HOMEODOMAINS (THE PROTEIN COMPONENT) BOUND TO ONE 14 BASE PAIR DNA DUPLEX IS THE MOLECULAR SPECIES ANALYZED IN THIS STUDY. EACH OF THE DNA DUPLEX AND THE COMPLEX HAS PSEUDO TWO-FOLD SYMMETRY ABOUT ITS CENTER. THE ASYMMETRIC UNIT CONTAINS 1.5 COMPLEXES, ONE OF WHICH IS COMPLETELY CONTAINED WITHIN THE ASYMMETRIC UNIT AND THE OTHER OF IS BISECTED AT ITS CENTER OF SYMMETRY BY A CRYSTALLOGRAPHIC TWO-FOLD AXIS. THE TWO-FOLD AVERAGED COMPLEX WAS MODELED AS A COMPLETE SINGLE HOMEODOMAIN AND A COMPLETE SINGLE STRAND OF THE DUPLEX. THEREFORE, THE MODEL CONTAINS THREE HOMEODOMAINS AND THREE DNA STRANDS. |
-Components
#1: Protein | Mass: 9716.782 Da / Num. of mol.: 3 / Fragment: HOMEODOMAIN / Mutation: C, C4S, S50Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: P06601 #2: DNA chain | | Mass: 4262.816 Da / Num. of mol.: 1 / Source method: obtained synthetically #3: DNA chain | | Mass: 4293.827 Da / Num. of mol.: 1 / Source method: obtained synthetically #4: DNA chain | | Mass: 4269.801 Da / Num. of mol.: 1 / Source method: obtained synthetically #5: Water | ChemComp-HOH / | Sequence details | THE STANDARD HOMEODOMAIN NUMBERING SYSTEM (SEE, FOR EXAMPLE, KISSINGER, C.R., LIU, B., MARTIN- ...THE STANDARD HOMEODOMAI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.09 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5.5 / Method: unknown | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. obs: 28315 / % possible obs: 92.9 % / Num. measured all: 94960 / Rmerge(I) obs: 0.058 |
Reflection shell | *PLUS % possible obs: 83.3 % / Rmerge(I) obs: 0.185 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor Rwork: 0.198 / Rfactor obs: 0.198 / Highest resolution: 2 Å Details: THE FOLLOWING SIDE CHAINS HAVE BEEN OMITTED FROM THE MODEL BECAUSE THEIR CONFORMATION WAS NOT EVIDENT FROM ELECTRON DENSITY MAPS: HOMEODOMAIN NO. 1: RESIDUES 122, 133, 158. HOMEODOMAIN NO. 2: ...Details: THE FOLLOWING SIDE CHAINS HAVE BEEN OMITTED FROM THE MODEL BECAUSE THEIR CONFORMATION WAS NOT EVIDENT FROM ELECTRON DENSITY MAPS: HOMEODOMAIN NO. 1: RESIDUES 122, 133, 158. HOMEODOMAIN NO. 2: RESIDUES 233, 236, 239, 255, 258. HOMEODOMAIN NO. 3: RESIDUES 300, 324, 357, 358. DUE TO THE TWO-FOLD AVERAGING OF THE DNA DUPLEXES, ALTERNATE SIDE CHAIN IDENTITIES HAVE BEEN MODELED IN THE FOLLOWING WAY: ALTERNATE SIDE CHAIN FOR RESIDUE A D 1A: RESIDUE T D 1B ALTERNATE SIDE CHAIN FOR RESIDUE T D 8A: RESIDUE A D 8B ALTERNATE SIDE CHAIN FOR RESIDUE T E 1A: RESIDUE A E 1B ALTERNATE SIDE CHAIN FOR RESIDUE A E 8A: RESIDUE T E 8B ALTERNATE SIDE CHAIN FOR RESIDUE T F 1A: RESIDUE A F 1B ALTERNATE SIDE CHAIN FOR RESIDUE T F 8A: RESIDUE A F 8B TWO OF THE WATER MOLECULES ARE EXCLUDED BY ONE OF THE TWO ALTERNATE SIDE CHAINS AT DNA RESIDUES NO. 408 AND 508, AS FOLLOWS: WATER RESIDUE NO. 941 IS PRESENT WITH THE ALTERNATE SIDE CHAIN REPRESENTED BY RESIDUE 508 BUT NOT 528. WATER RESIDUE NO. 942 IS PRESENT WITH THE ALTERNATE SIDE CHAIN REPRESENTED BY RESIDUE 428 BUT NOT 408. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 6 Å / Rfactor obs: 0.197 / Rfactor Rfree: 0.27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 38 Å2 |