[English] 日本語
Yorodumi- PDB-3f8l: Crystal Structure of the Effector Domain of PhnF from Mycobacteri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f8l | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Effector Domain of PhnF from Mycobacterium smegmatis | ||||||
Components | HTH-type transcriptional repressor phnF | ||||||
Keywords | TRANSCRIPTION / PhnF / GntR / HutC / regulator / UTRA / DNA-binding / Transcription regulation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Busby, J.N. / Gebhard, S. / Cook, G.M. / Baker, E.N. / Lott, S.J. / Money, V.A. | ||||||
Citation | Journal: To be Published Title: Crystal structure of PhnF, a GntR-family transcription regulator in Mycobacterium smegmatis Authors: Busby, J.N. / Gebhard, S. / Cook, G.M. / Baker, E.N. / Lott, S.J. / Money, V.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3f8l.cif.gz | 154.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3f8l.ent.gz | 120.7 KB | Display | PDB format |
PDBx/mmJSON format | 3f8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/3f8l ftp://data.pdbj.org/pub/pdb/validation_reports/f8/3f8l | HTTPS FTP |
---|
-Related structure data
Related structure data | 3f8mC 2p19S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||
2 |
| |||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Refine code: 4 / Label seq-ID: 1 - 162
|
-Components
#1: Protein | Mass: 22152.977 Da / Num. of mol.: 4 / Fragment: UNP residues 82-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: Mc2155 / Gene: MSMEG_0650, phnF / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QQ72 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.43 % / Mosaicity: 0.565 ° |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Micro-seeded into 0.65M ammonium sulfate, 0.1M lithium sulfate, 0.1M tris, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 4, 2008 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25.28 Å / Num. all: 68334 / Num. obs: 68334 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 1.6 / Num. unique all: 9909 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2P19 Resolution: 1.9→25.1 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.184 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.901 / SU B: 2.381 / SU ML: 0.07 / SU R Cruickshank DPI: 0.13 / SU Rfree: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.52 Å2 / Biso mean: 30.244 Å2 / Biso min: 4.87 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→25.1 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Ens-ID: 1 / Number: 1205 / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
|