+Open data
-Basic information
Entry | Database: PDB / ID: 1du0 | ||||||
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Title | ENGRAILED HOMEODOMAIN Q50A VARIANT DNA COMPLEX | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / homeodomain / DNA-binding protein / protein-DNA complex / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information posterior compartment specification / analia development / anterior head segmentation / posterior head segmentation / anterior/posterior lineage restriction, imaginal disc / trunk segmentation / genital disc development / genital disc anterior/posterior pattern formation / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation ...posterior compartment specification / analia development / anterior head segmentation / posterior head segmentation / anterior/posterior lineage restriction, imaginal disc / trunk segmentation / genital disc development / genital disc anterior/posterior pattern formation / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation / wing disc morphogenesis / neuroblast fate determination / imaginal disc-derived wing vein specification / segment polarity determination / ventral midline development / compartment pattern specification / gonad development / axon guidance / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / neuron differentiation / regulation of gene expression / sequence-specific DNA binding / negative regulation of neuron apoptotic process / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Grant, R.A. / Rould, M.A. / Klemm, J.D. / Pabo, C.O. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Exploring the role of glutamine 50 in the homeodomain-DNA interface: crystal structure of engrailed (Gln50 --> ala) complex at 2.0 A. Authors: Grant, R.A. / Rould, M.A. / Klemm, J.D. / Pabo, C.O. #1: Journal: J.Mol.Biol. / Year: 1998 Title: Engrailed homeodomain-DNA complex at 2.2 Angstroms resolution: A detailed view of the interface and comparison with other engrailed structures Authors: Fraenkel, E. / Rould, M.A. / Chambers, K.A. / Pabo, C.O. #2: Journal: Structure / Year: 1997 Title: Engrailed (gln50->lys) homeodomain-DNA complex at 1.9 Angstroms resolution: structural basis for enhanced affinity and altered specificity Authors: Tucker-Kellogg, L. / Rould, M.A. / Chambers, K.A. / Ades, S.E. / Sauer, R.T. #3: Journal: Biochemistry / Year: 1994 Title: Differential DNA-binding specificity of the engrailed homeodomain: the role of residue 50 Authors: Ades, S.E. / Sauer, R.T. #4: Journal: Cell(Cambridge,Mass.) / Year: 1990 Title: Crystal structure of an engrailed homeodomain-DNA comples at 2.8 Angstroms resolution: a framework for understanding homeodomain-DNA interactions Authors: Kissinger, C.A. / Liu, B. / Martin-Blanco, E. / Kornberg, T.B. / 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 | 1du0.cif.gz | 60.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1du0.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 1du0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1du0_validation.pdf.gz | 385.2 KB | Display | wwPDB validaton report |
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Full document | 1du0_full_validation.pdf.gz | 388.5 KB | Display | |
Data in XML | 1du0_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 1du0_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/1du0 ftp://data.pdbj.org/pub/pdb/validation_reports/du/1du0 | HTTPS FTP |
-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: DNA chain | Mass: 6387.157 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 6494.248 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 6907.921 Da / Num. of mol.: 2 / Mutation: GLN50ALA Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: P02836 #4: 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: 3.31 Å3/Da / Density % sol: 62.8 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: bis-Tris-propane, PEG 400, ammonium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 128 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 24, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 23204 / Num. obs: 23204 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.039 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.351 / Num. unique all: 1697 / % possible all: 70.3 |
Reflection | *PLUS Num. measured all: 115772 |
Reflection shell | *PLUS % possible obs: 70.3 % / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Resolution: 2→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): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 39.7 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.025 / 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 Rfactor Rfree: 0.269 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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