+Open data
-Basic information
Entry | Database: PDB / ID: 1lt0 | |||||||||
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Title | Crystal structure of the CN-bound BjFixL heme domain | |||||||||
Components | Sensor protein FixL | |||||||||
Keywords | TRANSFERASE / PAS fold | |||||||||
Function / homology | Function and homology information histidine phosphotransfer kinase activity / nitrogen fixation / histidine kinase / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Bradyrhizobium japonicum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å | |||||||||
Authors | Hao, B. / Isaza, C. / Arndt, J. / Soltis, M. / Chan, M.K. | |||||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Structure-based mechanism of O2 sensing and ligand discrimination by the FixL heme domain of Bradyrhizobium japonicum Authors: Hao, B. / Isaza, C. / Arndt, J. / Soltis, M. / Chan, M.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lt0.cif.gz | 38.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lt0.ent.gz | 26.1 KB | Display | PDB format |
PDBx/mmJSON format | 1lt0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/1lt0 ftp://data.pdbj.org/pub/pdb/validation_reports/lt/1lt0 | HTTPS FTP |
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-Related structure data
Related structure data | 1lsvC 1lswC 1lsxC 1drmS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 14919.858 Da / Num. of mol.: 1 / Fragment: Heme domain (residues 141-270) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Gene: FixL / Plasmid: pBH32 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 References: UniProt: P23222, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor |
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#2: Chemical | ChemComp-CYN / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.91 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: SODIUM CHLORIDE, MPD, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusionDetails: Gong, W., (1998) Proc. Natl. Acad. Sci. U.S.A., 95, 15177. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 28, 2000 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. all: 7182 / Num. obs: 7032 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.032 / Rsym value: 0.032 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 2.4→2.48 Å / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 7 / Num. unique all: 900 / Rsym value: 0.221 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.4 Å / Num. obs: 7182 / Num. measured all: 26220 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1DRM Resolution: 2.4→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 18.8 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.51 Å
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Refinement | *PLUS Highest resolution: 2.4 Å / % reflection Rfree: 8 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |