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Yorodumi- PDB-1i1g: CRYSTAL STRUCTURE OF THE LRP-LIKE TRANSCRIPTIONAL REGULATOR FROM ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i1g | ||||||
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Title | CRYSTAL STRUCTURE OF THE LRP-LIKE TRANSCRIPTIONAL REGULATOR FROM THE ARCHAEON PYROCOCCUS FURIOSUS | ||||||
Components | TRANSCRIPTIONAL REGULATOR LRPA | ||||||
Keywords | TRANSCRIPTION / helix-turn-helix / Lrp/AsnC family / Pyrococcus furiosus / transcriptional regulator | ||||||
Function / homology | Function and homology information sequence-specific DNA binding / DNA-binding transcription factor activity Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.9 Å | ||||||
Authors | Leonard, P.M. / Smits, S.H.J. / Sedelnikova, S.E. / Brinkman, A.B. / de Vos, W.M. / van der Oost, J. / Rice, D.W. / Rafferty, J.B. | ||||||
Citation | Journal: EMBO J. / Year: 2001 Title: Crystal structure of the Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus. Authors: Leonard, P.M. / Smits, S.H. / Sedelnikova, S.E. / Brinkman, A.B. / de Vos, W.M. / van der Oost, J. / Rice, D.W. / Rafferty, J.B. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AT PRESENT IT IS UNCLEAR WHETHER THE BIOLOGICAL UNIT IS A DIMER OR OCTAMER. COORDINATES FOR A COMPLETE BIOLOGICAL DIMER CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS ONE AND FOUR LISTED IN REMARK 350 TO SUBUNIT A IN THE ASYMMETRIC UNIT, OR BY APPLYING BIOMT TRANSFORMATIONS ONE AND THREE TO SUBUNIT B. COORDINATES FOR A COMPLETE BIOLOGICAL OCTAMER CAN BE GENERATED BY APPLYING ALL FOUR BIOMT TRANSFORMATIONS TO SUBUNITS A AND B IN THE ASYMMETRIC UNIT. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i1g.cif.gz | 57 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i1g.ent.gz | 41.4 KB | Display | PDB format |
PDBx/mmJSON format | 1i1g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/1i1g ftp://data.pdbj.org/pub/pdb/validation_reports/i1/1i1g | HTTPS FTP |
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-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: Protein | Mass: 15917.790 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: P42180 |
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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: 4.94 Å3/Da / Density % sol: 75.12 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6 Details: ammonium sulphate, sodium citrate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.3 / Method: vapor diffusionDetails: Sedelnikova, S.E., (2001) Acta Crystallogr, D57, 886. | ||||||||||||||||||||||||||||||||||||||||||
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: SRS / Beamline: PX7.2 / Wavelength: 1.488 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 4, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. all: 13809 / Num. obs: 13809 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 73.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.9→2.97 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.346 / % possible all: 94.7 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 30436 |
Reflection shell | *PLUS % possible obs: 96.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.9→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 20 Å / σ(F): 0 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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