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Yorodumi- PDB-1h9t: FADR, FATTY ACID RESPONSIVE TRANSCRIPTION FACTOR FROM E. COLI IN ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h9t | |||||||||
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Title | FADR, FATTY ACID RESPONSIVE TRANSCRIPTION FACTOR FROM E. COLI IN COMPLEX WITH FADB OPERATOR | |||||||||
Components |
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Keywords | TRANSCRIPTIONAL REGULATION | |||||||||
Function / homology | Function and homology information fatty-acyl-CoA binding / regulation of fatty acid metabolic process / positive regulation of fatty acid biosynthetic process / fatty acid metabolic process / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / cytosol Similarity search - Function | |||||||||
Biological species | ESCHERICHIA COLI (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | |||||||||
Authors | Van Aalten, D.M.F. / Dirusso, C.C. / Knudsen, J. | |||||||||
Citation | Journal: Embo J. / Year: 2001 Title: The Structural Basis of Acyl Coenzyme A-Dependent Regulation of the Transcription Factor Fadr Authors: Van Aalten, D.M.F. / Dirusso, C.C. / Knudsen, J. #1: Journal: Embo J. / Year: 2000 Title: Crystal Structure of Fadr, a Fatty Acid-Responsive Transcription Factor with a Novel Acyl Coenzyme A-Binding Fold Authors: Van Aalten, D.M. / Dirusso, C.C. / Knudsen, J. / Wierenga, R.K. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallization and X-Ray Diffraction Studies of the Fatty-Acid Responsive Transcription Factor Fadr from Escherichia Coli Authors: Van Aalten, D.M.F. / Knudsen, J. / Dirusso, C.C. / Kokko, T. / Wierenga, R.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h9t.cif.gz | 126.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h9t.ent.gz | 95.2 KB | Display | PDB format |
PDBx/mmJSON format | 1h9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/1h9t ftp://data.pdbj.org/pub/pdb/validation_reports/h9/1h9t | HTTPS FTP |
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-Related structure data
Related structure data | 1h9gC 1e2xS S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99886, -0.0443, -0.00809), Vector: Details | PROTEIN AND THE TWO DNA CHAINS | |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27493.111 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P09371, UniProt: P0A8V6*PLUS |
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-DNA chain , 2 types, 2 molecules XY
#2: DNA chain | Mass: 5789.762 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 5860.796 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 30 molecules
#4: Chemical | #5: Chemical | #6: 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: 2.48 Å3/Da / Density % sol: 60.77 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: SODIUM CITRATE PH 6.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
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: F2 / Wavelength: 1.02467 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 29, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02467 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→25 Å / Num. obs: 88082 / % possible obs: 98 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 3.25→3.38 Å / Redundancy: 5 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.5 / % possible all: 98.6 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. obs: 14138 / Num. measured all: 88082 |
Reflection shell | *PLUS % possible obs: 98.6 % / Redundancy: 4.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1E2X Resolution: 3.25→12 Å / SU B: 32 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0
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Displacement parameters | Biso mean: 66.611 Å2
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Refinement step | Cycle: LAST / Resolution: 3.25→12 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.32 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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