+Open data
-Basic information
Entry | Database: PDB / ID: 9ant | ||||||
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Title | ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / HOMEODOMAIN / DNA-BINDING PROTEIN / COMPLEX (HOMEODOMAIN-DNA) / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information specification of segmental identity, antennal segment / specification of segmental identity, thorax / neuroblast development / muscle cell fate specification / lymph gland development / ventral cord development / anterior/posterior axis specification / anterior/posterior pattern specification / midgut development / regulation of neurogenesis ...specification of segmental identity, antennal segment / specification of segmental identity, thorax / neuroblast development / muscle cell fate specification / lymph gland development / ventral cord development / anterior/posterior axis specification / anterior/posterior pattern specification / midgut development / regulation of neurogenesis / heart development / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.4 Å | ||||||
Authors | Fraenkel, E. / Pabo, C.O. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex. Authors: Fraenkel, E. / Pabo, C.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9ant.cif.gz | 71.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9ant.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 9ant.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9ant_validation.pdf.gz | 395.9 KB | Display | wwPDB validaton report |
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Full document | 9ant_full_validation.pdf.gz | 402.1 KB | Display | |
Data in XML | 9ant_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | 9ant_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/9ant ftp://data.pdbj.org/pub/pdb/validation_reports/an/9ant | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 4651.062 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #2: DNA chain | Mass: 4525.944 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #3: Protein | Mass: 8090.411 Da / Num. of mol.: 2 / Fragment: HOMEODOMAIN / Mutation: C39S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: P02833 #4: Chemical | ChemComp-NI / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 68 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 1-5% MPD 20 MM BIS-TRIS-PROPANE, PH 7.0 10 MM NICL2 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 15, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 17753 / Num. obs: 17753 / Observed criterion σ(I): 0 |
Reflection | *PLUS % possible obs: 97.9 % / Num. measured all: 309545 / Rmerge(I) obs: 0.088 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.4→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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