+Open data
-Basic information
Entry | Database: PDB / ID: 1dp8 | ||||||
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Title | CRYSTAL STRUCTURE OF THE NITRIC OXIDE BOUND FIXL HEME DOMAIN | ||||||
Components | FIXL PROTEIN | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / HEME / FIXL HEME DOMAIN LIGANDED STRUCTURES / HISTIDINE KINASE / SIGNAL TRANSDUCTION / TWO COMPONENT SYSTEM / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
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 / Resolution: 2.5 Å | ||||||
Authors | Gong, W. / Hao, B. / Chan, M.K. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: New mechanistic insights from structural studies of the oxygen-sensing domain of Bradyrhizobium japonicum FixL. Authors: Gong, W. / Hao, B. / Chan, M.K. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: Structure of a Biological Oxygen Sensor: a New Mechanism for Heme-driven Signal Transduction Authors: Gong, W. / Hao, B. / Mansy, S.S. / Gonzalez, G. / Gilles-Gonzalez, M.A. / 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 | 1dp8.cif.gz | 40.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dp8.ent.gz | 27.1 KB | Display | PDB format |
PDBx/mmJSON format | 1dp8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dp8_validation.pdf.gz | 473 KB | Display | wwPDB validaton report |
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Full document | 1dp8_full_validation.pdf.gz | 475.4 KB | Display | |
Data in XML | 1dp8_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | 1dp8_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/1dp8 ftp://data.pdbj.org/pub/pdb/validation_reports/dp/1dp8 | HTTPS FTP |
-Related structure data
Related structure data | 1dp6C 1dp9C 1bv5 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Plasmid: PRJ7349 / Production host: Escherichia coli (E. coli) / References: UniProt: P23222 |
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#2: Chemical | ChemComp-NO / |
#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: 3.04 Å3/Da / Density % sol: 59.48 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Sodium Chloride, HEPES, MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion / Details: W, Gong, (1998) Proc.Natl.Acad.Sci.USA, 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: NSLS / Beamline: X4A / Wavelength: 1.283 |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.283 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 45555 / Num. obs: 6138 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 2.5→20 Å / Rmerge(I) obs: 0.293 / Num. unique all: 6138 / % possible all: 92.3 |
Reflection | *PLUS Num. measured all: 45555 |
Reflection shell | *PLUS % possible obs: 92.3 % |
-Processing
Software |
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Refinement | Resolution: 2.5→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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