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Yorodumi- PDB-3clk: Crystal structure of a transcription regulator from Lactobacillus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3clk | ||||||
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Title | Crystal structure of a transcription regulator from Lactobacillus plantarum | ||||||
Components | Transcription regulator | ||||||
Keywords | TRANSCRIPTION REGULATOR / 11017j / PSI-II / NYSGXRC / dimer / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / DNA-binding / Transcription / Transcription regulation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lactobacillus plantarum WCFS1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å | ||||||
Authors | Sugadev, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a transcription regulator from lactobacillus plantarum. Authors: Sugadev, R. / 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 | 3clk.cif.gz | 111.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3clk.ent.gz | 89.9 KB | Display | PDB format |
PDBx/mmJSON format | 3clk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3clk_validation.pdf.gz | 449.2 KB | Display | wwPDB validaton report |
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Full document | 3clk_full_validation.pdf.gz | 461.3 KB | Display | |
Data in XML | 3clk_validation.xml.gz | 23 KB | Display | |
Data in CIF | 3clk_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/3clk ftp://data.pdbj.org/pub/pdb/validation_reports/cl/3clk | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32177.217 Da / Num. of mol.: 2 / Fragment: Residues 57-335 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus plantarum WCFS1 (bacteria) Species: Lactobacillus plantarum / Strain: WCFS1 / NCIMB 8826 / Plasmid: pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q88S23, UniProt: F9ULH5*PLUS #2: Chemical | ChemComp-GOL / | #3: 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: 2.11 Å3/Da / Density % sol: 41.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Bis-Tris pH 6.5, 25% PEG MME 2000, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 8, 2008 / Details: Mirrors |
Radiation | Monochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→50 Å / Num. all: 62919 / Num. obs: 62919 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 2.08→2.15 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.276 / Num. unique all: 6197 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.08→45.79 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 95014.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber Details: The Friedel pairs were used in phasing. 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 ...Details: The Friedel pairs were used in phasing. 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: 43.0969 Å2 / ksol: 0.340233 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.08→45.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.08→2.21 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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