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Yorodumi- PDB-5h1a: Crystal structure of an IclR homolog from Microbacterium sp. stra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h1a | ||||||
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Title | Crystal structure of an IclR homolog from Microbacterium sp. strain HM58-2 | ||||||
Components | IclR transcription factor homolog | ||||||
Keywords | TRANSCRIPTION REGULATOR / DNA-binding | ||||||
Function / homology | PHOSPHATE ION Function and homology information | ||||||
Biological species | Microbacterium sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Akiyama, T. / Yamada, Y. / Takaya, N. / Ito, S. / Sasaki, Y. / Yajima, S. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017 Title: Crystal structure of an IclR homologue from Microbacterium sp. strain HM58-2. Authors: Akiyama, T. / Yamada, Y. / Takaya, N. / Ito, S. / Sasaki, Y. / Yajima, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h1a.cif.gz | 189.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h1a.ent.gz | 151.9 KB | Display | PDB format |
PDBx/mmJSON format | 5h1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/5h1a ftp://data.pdbj.org/pub/pdb/validation_reports/h1/5h1a | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 29323.725 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Microbacterium sp. (bacteria) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-PO4 / | #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: 2.51 Å3/Da / Density % sol: 50.92 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 8 / Details: 1M (NH4)2HPO4 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.038 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.038 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 69549 / % possible obs: 98.9 % / Redundancy: 6.7 % / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 2.1→2.14 Å |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→43.6 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.174 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.174 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→43.6 Å
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Refine LS restraints |
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