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Yorodumi- PDB-3hs3: Crystal structure of periplasmic binding ribose operon repressor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hs3 | ||||||
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Title | Crystal structure of periplasmic binding ribose operon repressor protein from Lactobacillus acidophilus | ||||||
Components | Ribose operon repressor | ||||||
Keywords | transcription regulator / PSI-II / NYSGXRC / 11235h / periplasmic binding protein / ribose operon repressor / 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 acidophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Agarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of periplasmic binding ribose operon repressor protein from Lactobacillus acidophilus Authors: Agarwal, 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 | 3hs3.cif.gz | 119.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hs3.ent.gz | 93.5 KB | Display | PDB format |
PDBx/mmJSON format | 3hs3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/3hs3 ftp://data.pdbj.org/pub/pdb/validation_reports/hs/3hs3 | 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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1 |
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Unit cell |
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Details | Dimer |
-Components
#1: Protein | Mass: 31265.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Strain: NCFM / Gene: rbsR, LBA1472 / Plasmid: pSGX3(BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)RIPL / References: UniProt: Q5FJ32 #2: 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: 2.33 Å3/Da / Density % sol: 47.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris, 2M Ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2009 / Details: mirrors |
Radiation | Monochromator: Si-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 77464 / Num. obs: 77464 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 6 / Num. unique all: 3813 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: None Resolution: 1.6→43.2 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 164239.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: selenomet protein was used in structure determination.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.4381 Å2 / ksol: 0.37994 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→43.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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