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Yorodumi- PDB-2aac: ESCHERCHIA COLI GENE REGULATORY PROTEIN ARAC COMPLEXED WITH D-FUCOSE -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aac | ||||||
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Title | ESCHERCHIA COLI GENE REGULATORY PROTEIN ARAC COMPLEXED WITH D-FUCOSE | ||||||
Components | ARAC | ||||||
Keywords | TRANSCRIPTION FACTOR / CARBOHYDRATE BINDING / COILED-COIL / JELLY ROLL | ||||||
Function / homology | Function and homology information arabinose catabolic process / DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / RIGID-BODY REFINEMENT, DIFFERENCE FOURIER MAPS / Resolution: 1.6 Å | ||||||
Authors | Soisson, S.M. / Wolberger, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: The 1.6 A crystal structure of the AraC sugar-binding and dimerization domain complexed with D-fucose. Authors: Soisson, S.M. / MacDougall-Shackleton, B. / Schleif, R. / Wolberger, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2aac.cif.gz | 83.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aac.ent.gz | 65 KB | Display | PDB format |
PDBx/mmJSON format | 2aac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/2aac ftp://data.pdbj.org/pub/pdb/validation_reports/aa/2aac | HTTPS FTP |
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-Related structure data
Related structure data | 2arcS S: Starting model for refinement |
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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: (-0.191475, 0.4722, -0.860444), Vector: |
-Components
#1: Protein | Mass: 20547.184 Da / Num. of mol.: 2 / Fragment: SUGAR-BINDING/DIMERIZATION Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ARAC / Gene (production host): ARAC / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9E0 #2: Sugar | #3: Chemical | #4: 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: 2.23 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||
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Crystal grow | pH: 5.5 Details: PROTEIN WAS CRYSTALLIZED BY MICROSEEDING FROM 24% PEG 4000, 100 MM SODIUM CITRATE PH 5.5 200 MM AMMONIUM ACETATE | ||||||||||||||||||||
Crystal grow | *PLUS pH: 7.25 / Method: vapor diffusion, hanging dropDetails: used to seeding, Soisson, S.M., (1997) Science, 276, 421. | ||||||||||||||||||||
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: NSLS / Beamline: X4A / Wavelength: 0.689 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Sep 1, 1995 / Details: SPHERICAL RH COATED MIRROR |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) DOUBLE CRYSTAL MONOCHROMATOR Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.689 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 47363 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 12.31 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.6→1.67 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.39 / % possible all: 99 |
Reflection | *PLUS Num. obs: 57378 / Num. measured all: 293876 / Rmerge(I) obs: 0.09 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID-BODY REFINEMENT, DIFFERENCE FOURIER MAPS Starting model: PDB ENTRY 2ARC Resolution: 1.6→7 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 12.48 Å2
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Refine analyze | Luzzati coordinate error obs: 0.15 Å / Luzzati d res low obs: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.67 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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