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Yorodumi- PDB-3bbl: Crystal structure of a regulatory protein of LacI family from Chl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bbl | ||||||
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Title | Crystal structure of a regulatory protein of LacI family from Chloroflexus aggregans | ||||||
Components | Regulatory protein of LacI family | ||||||
Keywords | REGULATORY PROTEIN / Protein Structure Initiative II / PSI-II / NYSGXRC / Transcriptional regulator / Periplasmic binding protein / LacI family / Structural Genomics / New York SGX Research Center for Structural Genomics / DNA-binding / Transcription regulation | ||||||
Function / homology | Function and homology information alanine racemase / alanine racemase activity / regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | Chloroflexus aggregans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å | ||||||
Authors | Kumaran, D. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a regulatory protein of LacI family from the Chloroflexus aggregans. Authors: Kumaran, D. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bbl.cif.gz | 67.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bbl.ent.gz | 53.1 KB | Display | PDB format |
PDBx/mmJSON format | 3bbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/3bbl ftp://data.pdbj.org/pub/pdb/validation_reports/bb/3bbl | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32701.789 Da / Num. of mol.: 1 / Fragment: Residues 63-338 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chloroflexus aggregans (bacteria) / Strain: DSM 9485 / Gene: CaggDRAFT_0381 / Plasmid: pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0H3S5, UniProt: B8GD81*PLUS | ||
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#2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.09 Å3/Da / Density % sol: 69.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 5% PEG 2000, 40% Tacsimate, 5% Ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2007 / Details: Mirrors |
Radiation | Monochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 22738 / Num. obs: 22738 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.4 % / Biso Wilson estimate: 20.1 Å2 / Rsym value: 0.1 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 2 / Num. unique all: 1810 / Rsym value: 0.37 / % possible all: 79 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.35→35.38 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 43502.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.7922 Å2 / ksol: 0.369769 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→35.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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