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- PDB-2f8d: BenM effector-Binding domain crystallized from high pH conditions -
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Open data
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Basic information
Entry | Database: PDB / ID: 2f8d | ||||||
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Title | BenM effector-Binding domain crystallized from high pH conditions | ||||||
![]() | HTH-type transcriptional regulator benM | ||||||
![]() | GENE REGULATION / BenM / LTTR / LysR-type transcriptional regulator / tetramerization / Effector binding domain / Inducer binding domain | ||||||
Function / homology | ![]() : / protein-DNA complex / DNA-binding transcription factor activity / DNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ezezika, O.C. / Haddad, S. / Neidle, E.L. / Momany, C. | ||||||
![]() | ![]() Title: Oligomerization of BenM, a LysR-type transcriptional regulator: structural basis for the aggregation of proteins in this family. Authors: Ezezika, O.C. / Haddad, S. / Neidle, E.L. / Momany, C. #1: ![]() Title: Crystallization of the effector-binding domains of BenM and BenM, LysR-type transcriptional regulators from Acinetobacter sp. ADP1. Authors: Clark, T. / Haddad, S. / Neidle, E. / Momany, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.5 KB | Display | ![]() |
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PDB format | ![]() | 86.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2f97C ![]() 2f6gS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The biological unit is a dimer. A dimer is in the asymmetric unit. |
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Components
#1: Protein | Mass: 26401.447 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.6 Å3/Da / Density % sol: 73.1 % |
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Crystal grow | pH: 10 Details: PEG 4000, glycerol, imidazole, tris, CAPS, KBr, NaCl, benzoate, pH 10, Microbatch under oil |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 1, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→92.06 Å / Num. all: 25480 / Num. obs: 25480 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.16 % / Biso Wilson estimate: 53.78698 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 2.7→2.8 Å / % possible obs: 98.1 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 5.85 / Num. measured obs: 2494 / Num. unique all: 2494 / Rsym value: 0 / Χ2: 1.355 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2F6G Resolution: 2.7→92.06 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.933 / SU B: 12.356 / SU ML: 0.139 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.221 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 32.036 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→92.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.695→2.765 Å / Total num. of bins used: 20
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