+Open data
-Basic information
Entry | Database: PDB / ID: 1xbr | ||||||
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Title | T DOMAIN FROM XENOPUS LAEVIS BOUND TO DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / COMPLEX (TRANSCRIPTION FACTOR-DNA) / TRANSCRIPTION FACTOR / DNA-BINDING PROTEIN / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / embryonic axis specification / cellular response to fibroblast growth factor stimulus / determination of left/right symmetry / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å | ||||||
Authors | Muller, C.W. | ||||||
Citation | Journal: Nature / Year: 1997 Title: Crystallographic structure of the T domain-DNA complex of the Brachyury transcription factor. Authors: Muller, C.W. / Herrmann, B.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xbr.cif.gz | 115.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xbr.ent.gz | 86.3 KB | Display | PDB format |
PDBx/mmJSON format | 1xbr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xbr_validation.pdf.gz | 381.7 KB | Display | wwPDB validaton report |
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Full document | 1xbr_full_validation.pdf.gz | 388.7 KB | Display | |
Data in XML | 1xbr_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 1xbr_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/1xbr ftp://data.pdbj.org/pub/pdb/validation_reports/xb/1xbr | 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper: (Code: given Matrix: (-0.999762, 0.020839, 0.006386), Vector: |
-Components
#1: DNA chain | Mass: 7367.791 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Description: PALINDROMIC BINDING SITE OF THE T DOMAIN FROM AN IN VITRO SELECTION EXPERIMENT #2: Protein | Mass: 21074.268 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Tissue: EMBRYO Description: EUKARYOTIC TRANSCRIPTION FACTOR, TRANSIENTLY EXPRESSED IN THE EMBRYO, REQUIRED FOR MESODERM FORMATION Gene: XBRA / Plasmid: PT7-7 (NOVAGEN) / Species (production host): Escherichia coli / Cellular location (production host): CYTOSOL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P24781 #3: 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: 2.45 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.2 Details: PROTEIN WAS CRYSTALLIZED FROM 2-8% PEG 8K, 20 MM MGCL2 50 MM NA-ACETATE, PH 4.2 1MM DTT, 5 MM SPERMINE, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: SI 111 CHANNEL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 22983 / % possible obs: 98.9 % / Redundancy: 4.4 % / Rsym value: 0.036 / Net I/σ(I): 33.5 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 13.7 / Rsym value: 0.136 / % possible all: 98.9 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / % possible obs: 98.9 % / Redundancy: 4.4 % / Num. measured all: 101653 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / % possible obs: 98.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 13.7 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.5→20 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 1000000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Rms dev Biso : 1.85 Å2 / Rms dev position: 0.32 Å / Weight Biso : 1 / Weight position: 10
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LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.306 |