[English] 日本語
![](img/lk-miru.gif)
- PDB-2h99: Crystal structure of the effector binding domain of a BenM varian... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2h99 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the effector binding domain of a BenM variant (R156H,T157S) | ||||||
![]() | HTH-type transcriptional regulator benM | ||||||
![]() | TRANSCRIPTION / LTTR / BenM / transcriptional regulation / CatM | ||||||
Function / homology | ![]() : / protein-DNA complex / DNA-binding transcription factor activity / DNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ezezika, O.C. / Craven, S.H. / Neidle, E.L. / Momany, C. | ||||||
![]() | ![]() Title: Inducer responses of BenM, a LysR-type transcriptional regulator from Acinetobacter baylyi ADP1. Authors: Craven, S.H. / Ezezika, O.C. / Haddad, S. / Hall, R.A. / Momany, C. / Neidle, E.L. #1: ![]() Title: Distinct Effector-binding Sites Enable Synergistic Transcriptional Activation By BenM, a LysR-type Regulator Authors: Ezezika, O.C. / Haddad, S. / Clark, T.J. / Neidle, E.L. / Momany, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 117.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 88.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 483.9 KB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 36.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2h9bC ![]() 3glbC ![]() 2f97S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological unit is a dimer |
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35611.961 Da / Num. of mol.: 2 / Fragment: Effector binding domain / Mutation: R156H, T157S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 590 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49.2 % |
---|---|
Crystal grow | Temperature: 288.2 K / Method: microbatch under oil Details: Precipitant: 0.015 M magnesium acetate, 0.05 M sodium cacodlylate, 1.7 M ammonium sulfate Protein: 20 mM tris HCl, 0.5 M NaCl, pH 7.9, 10% glycerol Equal volumes mixed, microbatch under oil. ...Details: Precipitant: 0.015 M magnesium acetate, 0.05 M sodium cacodlylate, 1.7 M ammonium sulfate Protein: 20 mM tris HCl, 0.5 M NaCl, pH 7.9, 10% glycerol Equal volumes mixed, microbatch under oil. The growing crystallization solution was in pH 6 and the protein solution was in pH 7.9 condition, temperature 288.2K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 22, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 44035 / % possible obs: 99.7 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.073 / Χ2: 0.925 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.85→1.92 Å / % possible obs: 99.3 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.484 / Num. unique obs: 4281 / Χ2: 0.754 / % possible all: 99.3 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB accession code 2F97, BenM-EBD (high pH) Resolution: 1.85→44 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.781 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.126 / ESU R Free: 0.121 / Stereochemistry target values: Engh & Huber / 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 mean: 19.128 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→44 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
|