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Yorodumi- PDB-1dp7: COCRYSTAL STRUCTURE OF RFX-DBD IN COMPLEX WITH ITS COGNATE X-BOX ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dp7 | ||||||
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Title | COCRYSTAL STRUCTURE OF RFX-DBD IN COMPLEX WITH ITS COGNATE X-BOX BINDING SITE | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / WINGED HELIX / MHC CLASS II TRANSCRIPTION FACTOR / PROTEIN-DNA COCRYSTAL STRUCTURE / NOVEL MODE OF DNA RECOGNITION / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / immune response / intracellular membrane-bounded organelle / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm Similarity search - Function | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å | ||||||
Authors | Gajiwala, K.S. / Chen, H. / Cornille, F. / Roques, B.P. / Reith, W. / Mach, B. / Burley, S.K. | ||||||
Citation | Journal: Nature / Year: 2000 Title: Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding. Authors: Gajiwala, K.S. / Chen, H. / Cornille, F. / Roques, B.P. / Reith, W. / Mach, B. / Burley, S.K. #1: Journal: Nature / Year: 1993 Title: Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5 Authors: Clark, K.L. / Halay, E.D. / Lai, E. / Burley, S.K. #2: Journal: Nature / Year: 1993 Title: Crystal structure of globular domain of histone H5 and its implications for nucleosome binding Authors: Ramakrishnan, V. / Finch, J. / Graziano, V. / Sweet, R. #3: Journal: Mol.Cell.Biol. / Year: 1996 Title: A consensus motif in the RFX DNA binding domain and binding domain mutants with altered specificity Authors: Emery, P. / Strubin, M. / Hofmann, K. / Bucher, P. / Mach, B. / Reith, W. #4: Journal: Mol.Cell.Biol. / Year: 1994 Title: RFX1, a transactivator of hepatitis B virus enhancer I, belongs to a novel family of homodimeric and heterodimeric DNA-binding proteins Authors: Reith, W. / Ucla, C. / Barras, E. / Gaud, A. / Durand, B. / Herrero-Sanchez, C. / Kobr, M. / Mach, B. #5: Journal: Nucleic Acids Res. / Year: 1998 Title: DNA binding properties of a chemically synthesized DNA binding domain of hRFX1 Authors: Cornille, F. / Emery, P. / Schuler, W. / Lenoir, C. / Mach, B. / Roques, B.P. / Reith, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dp7.cif.gz | 44.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dp7.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 1dp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dp7_validation.pdf.gz | 443.1 KB | Display | wwPDB validaton report |
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Full document | 1dp7_full_validation.pdf.gz | 443.1 KB | Display | |
Data in XML | 1dp7_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 1dp7_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/1dp7 ftp://data.pdbj.org/pub/pdb/validation_reports/dp/1dp7 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 5027.931 Da / Num. of mol.: 1 / Fragment: X-BOX / Source method: obtained synthetically | ||||
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#2: Protein | Mass: 8829.081 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN / Mutation: C24N,C30S / Source method: obtained synthetically Details: SEQUENCE TAKEN FROM HUMAN MHC CLASS II TRANSCRIPTION FACTOR References: UniProt: P22670 | ||||
#3: Chemical | #4: Chemical | ChemComp-PEG / | #5: 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: 2.76 Å3/Da / Density % sol: 55.43 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 400, MAGNESIUM ACETATE, SODIUM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.5→10 Å / Num. obs: 22780 / % possible obs: 96.5 % / Observed criterion σ(I): 3 / Redundancy: 2 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.8 | |||||||||||||||
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2 % / Rmerge(I) obs: 0.472 / % possible all: 94.6 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 94.6 % |
-Processing
Software |
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Refinement | Resolution: 1.5→10 Å / Cross valid method: THROUGHOUT / σ(I): 3 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rwork: 0.216 |