[English] 日本語
Yorodumi- PDB-2vbx: Feast or famine regulatory protein (Rv3291c)from M. tuberculosis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vbx | ||||||
---|---|---|---|---|---|---|---|
Title | Feast or famine regulatory protein (Rv3291c)from M. tuberculosis complexed with L-Phenylalanine | ||||||
Components | TRANSCRIPTIONAL REGULATORY PROTEIN | ||||||
Keywords | DNA BINDING PROTEIN / FEAST/FAMINE REGULATORY PROTEIN / DNA-BINDING PROTEIN / TRANSCRIPTION REGULATOR / TRANSCRIPTION REGULATION / M. TUBERCULOSIS / HISTIDINE COMPLEX / LRP / RV3291C / DNA-BINDING / TRANSCRIPTION | ||||||
Function / homology | Function and homology information amino acid binding / protein homooligomerization / sequence-specific DNA binding / DNA binding Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIRAS / Resolution: 2.75 Å | ||||||
Authors | Shrivastava, T. / Ramachandran, R. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2007 Title: Mechanistic Insights from the Crystal Structures of a Feast/Famine Regulatory Protein from Mycobacterium Tuberculosis H37Rv. Authors: Shrivastava, T. / Ramachandran, R. | ||||||
History |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2vbx.cif.gz | 63.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2vbx.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vbx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/2vbx ftp://data.pdbj.org/pub/pdb/validation_reports/vb/2vbx | HTTPS FTP |
---|
-Related structure data
Related structure data | 2ivmC 2vbwC 2vbyC 2vbzC 2vc0C 2vc1C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 16530.596 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P96896 #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | L-HISTIDINE (HIS): L-HISTIDINE | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.52 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→20 Å / Num. obs: 13598 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.9 / % possible all: 99.7 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIRAS Starting model: NONE Resolution: 2.75→71.43 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.869 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-3 ARE DISORDERED IN THE STRUCTURE
| ||||||||||||||||||||
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: 36.83 Å2
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→71.43 Å
| ||||||||||||||||||||
LS refinement shell | Resolution: 2.75→2.82 Å / Total num. of bins used: 20 /
|