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Yorodumi- PDB-3dbi: CRYSTAL STRUCTURE OF SUGAR-BINDING TRANSCRIPTIONAL REGULATOR (LAC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dbi | ||||||
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Title | CRYSTAL STRUCTURE OF SUGAR-BINDING TRANSCRIPTIONAL REGULATOR (LACI FAMILY) FROM ESCHERICHIA COLI COMPLEXED WITH PHOSPHATE | ||||||
Components | SUGAR-BINDING TRANSCRIPTIONAL REGULATOR, LACI FAMILY | ||||||
Keywords | TRANSCRIPTION REGULATOR / STRUCTURAL GENOMICS / SUGAR-BINDING TRANSCRIPTIONAL REGULATOR / PROTEIN STRUCTURE INITIATIVE / PSI-2 / New York SGX Research Center for Structural Genomics / NYSGXRC / DNA-BINDING / TRANSCRIPTION REGULATION / Repressor / Transcription | ||||||
Function / homology | Function and homology information sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å | ||||||
Authors | Patskovsky, Y. / Ozyurt, S. / Freeman, J. / Wu, B. / Maletic, M. / Koss, J. / Wasserman, S.R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Sugar-Binding Transcriptional Regulator (LacI Family) from Escherichia Coli Complexed with Phosphate. Authors: Patskovsky, Y. / Ozyurt, S. / Freeman, J. / Wu, B. / Maletic, M. / Koss, J. / Wasserman, S.R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dbi.cif.gz | 171.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dbi.ent.gz | 144.6 KB | Display | PDB format |
PDBx/mmJSON format | 3dbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/3dbi ftp://data.pdbj.org/pub/pdb/validation_reports/db/3dbi | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
NCS ensembles :
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Details | authors state that the biological assembly is likely a dimer. |
-Components
#1: Protein | Mass: 37574.227 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Gene: LACI / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: P24242 #2: Chemical | #3: Chemical | ChemComp-GOL / | #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: 2.55 Å3/Da / Density % sol: 51.72 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 5 Details: 20% PEG3350 PH 7.0, 100MM DI-POTASSIU HYDROGEN PHOSPHATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, pH 5.00 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 30, 2008 |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 44638 / % possible obs: 100 % / Observed criterion σ(I): -0.5 / Redundancy: 13 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.45→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.919 / SU B: 9.261 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.361 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.05 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.451→2.514 Å / Total num. of bins used: 20
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