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Yorodumi- PDB-2h98: Crystal structure of the effector binding domain of a CatM varian... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h98 | ||||||
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Title | Crystal structure of the effector binding domain of a CatM variant, CatM(V158M) | ||||||
Components | HTH-type transcriptional regulator catM | ||||||
Keywords | TRANSCRIPTION / CatM / BenM / LTTR / Transcriptional regulator / Acinetobacter | ||||||
Function / homology | Function and homology information aromatic compound catabolic process / DNA-binding transcription factor activity / DNA binding Similarity search - Function | ||||||
Biological species | Acinetobacter sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ezezika, O.C. / Neidle, E.L. / Momany, C. | ||||||
Citation | Journal: To be Published Title: Structural basis for the altered regulatory roles of three LysR-type transcritional variants of CatM and BenM: CatM(V158M), CatM(R156H) and BenM(R156H/T157S) Authors: Ezezika, O.C. / Neidle, E.L. / Momany, C. #1: Journal: To be Published 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h98.cif.gz | 116.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h98.ent.gz | 86.8 KB | Display | PDB format |
PDBx/mmJSON format | 2h98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/2h98 ftp://data.pdbj.org/pub/pdb/validation_reports/h9/2h98 | HTTPS FTP |
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-Related structure data
Related structure data | 2f7bS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological unit is a dimer |
-Components
#1: Protein | Mass: 35430.273 Da / Num. of mol.: 2 / Fragment: Effector Binding domain / Mutation: V158M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter sp. (bacteria) / Strain: ADP1 / Gene: catM, catR / Plasmid: pET21B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07774 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 37.5 % |
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Crystal grow | Temperature: 296.4 K Details: Precipitant:0.1 M LiCL, 0.1 M MES, 40% PEG8000 Protein: 20 mM tris HCl, 0.5 M NaCl, 250 mM imidazole, pH 7.9, 10% glycerol Equal volumes mixed, Microbatch under oil. The growing ...Details: Precipitant:0.1 M LiCL, 0.1 M MES, 40% PEG8000 Protein: 20 mM tris HCl, 0.5 M NaCl, 250 mM imidazole, 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 296.4K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 9, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 56879 / Num. obs: 34934 / % possible obs: 94.5 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.045 / Χ2: 0.948 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible obs: 93 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 14.3 / Num. unique all: 5173 / Num. unique obs: 3450 / Χ2: 1.038 / % possible all: 89.87 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB accession code 2F7B, CatM-EBD Resolution: 1.8→44.2 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.681 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.159 / ESU R Free: 0.153 / 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: 8.918 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→44.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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