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Yorodumi- PDB-1d5y: CRYSTAL STRUCTURE OF THE E. COLI ROB TRANSCRIPTION FACTOR IN COMP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d5y | ||||||
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Title | CRYSTAL STRUCTURE OF THE E. COLI ROB TRANSCRIPTION FACTOR IN COMPLEX WITH DNA | ||||||
Components |
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Keywords | transcription/DNA / Protein-DNA complex / Rob Transcription factor / DNA / transcription-DNA COMPLEX | ||||||
Function / homology | Function and homology information sequence-specific DNA binding / DNA-binding transcription factor activity / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å | ||||||
Authors | Kwon, H.J. / Bennik, M.H.J. / Demple, B. / Ellenberger, T. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 Title: Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA. Authors: Kwon, H.J. / Bennik, M.H. / Demple, B. / Ellenberger, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d5y.cif.gz | 276.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d5y.ent.gz | 221.9 KB | Display | PDB format |
PDBx/mmJSON format | 1d5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d5y_validation.pdf.gz | 403 KB | Display | wwPDB validaton report |
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Full document | 1d5y_full_validation.pdf.gz | 453.9 KB | Display | |
Data in XML | 1d5y_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 1d5y_validation.cif.gz | 44.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/1d5y ftp://data.pdbj.org/pub/pdb/validation_reports/d5/1d5y | 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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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 6480.225 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 6404.144 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Protein | Mass: 33394.137 Da / Num. of mol.: 4 / Fragment: RESIDUES 3-289, KLAAA EXTENSION AFTER RESIDUE 289 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACI0 |
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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: 3.31 Å3/Da / Density % sol: 62.85 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Peg 8000, MES, MgCl2, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9161 |
Detector | Type: OTHER / Detector: CCD / Date: Jan 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9161 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 54476 / Num. obs: 54476 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.426 / Num. unique all: 4992 / % possible all: 87.2 |
Reflection | *PLUS Num. measured all: 306889 |
-Processing
Software |
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Refinement | Resolution: 2.7→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 7 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |