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Yorodumi- PDB-2rgy: Crystal structure of transcriptional regulator of LacI family fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rgy | ||||||
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Title | Crystal structure of transcriptional regulator of LacI family from Burkhoderia phymatum | ||||||
Components | Transcriptional regulator, LacI family | ||||||
Keywords | TRANSCRIPTION REGULATOR / 11011j / NYSGXRC / Transctiptional regulator / LacI family / sugar binding protein / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / DNA-binding / Transcription / 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 | Burkholderia phymatum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å | ||||||
Authors | Agarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Structural analysis of transcription regulator of LacI family from Burkholderia phymatum. 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 | 2rgy.cif.gz | 66.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rgy.ent.gz | 51.3 KB | Display | PDB format |
PDBx/mmJSON format | 2rgy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rgy_validation.pdf.gz | 420.8 KB | Display | wwPDB validaton report |
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Full document | 2rgy_full_validation.pdf.gz | 424.2 KB | Display | |
Data in XML | 2rgy_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 2rgy_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/2rgy ftp://data.pdbj.org/pub/pdb/validation_reports/rg/2rgy | 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: 32167.475 Da / Num. of mol.: 1 / Fragment: Residues 81-359 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia phymatum (bacteria) / Strain: STM815 / Gene: BphyDRAFT_4885 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: A0FW12, UniProt: B2JNW3*PLUS |
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#2: 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: 2.33 Å3/Da / Density % sol: 47.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Magnesium chloride, 0.1M Bis-tris, 25% PEG 3350, pH 6.5, 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: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 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: 2.05→50 Å / Num. all: 19243 / Num. obs: 19243 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 12.7 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 2 / Num. unique all: 1892 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.05→42.72 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 100792.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / 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: 36.8927 Å2 / ksol: 0.349963 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→42.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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