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Yorodumi- PDB-1u55: Crystal structure of an oxygen binding H-NOX domain related to so... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u55 | ||||||
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Title | Crystal structure of an oxygen binding H-NOX domain related to soluble guanylate cyclases (oxygen complex) | ||||||
Components | Heme-based Methyl-accepting Chemotaxis Protein | ||||||
Keywords | SIGNALING PROTEIN / H-NOX domain / Heme / Oxygen sensor / Signal transduction / Chemotaxis | ||||||
Function / homology | Function and homology information lysozyme activity / heme binding / signal transduction / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Thermoanaerobacter tengcongensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Pellicena, P. / Karow, D.S. / Boon, E.M. / Marletta, M.A. / Kuriyan, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2004 Title: Crystal structure of an oxygen-binding heme domain related to soluble guanylate cyclases. Authors: Pellicena, P. / Karow, D.S. / Boon, E.M. / Marletta, M.A. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u55.cif.gz | 97.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u55.ent.gz | 73.6 KB | Display | PDB format |
PDBx/mmJSON format | 1u55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/1u55 ftp://data.pdbj.org/pub/pdb/validation_reports/u5/1u55 | HTTPS FTP |
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-Related structure data
Related structure data | 1u4hSC 1u56C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22047.502 Da / Num. of mol.: 2 / Fragment: H-NOX domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria) Gene: Tar4 / Plasmid: pet20b / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner BL21(DE3) pLysS / References: UniProt: Q8RBX6 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: 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: 2.8 Å3/Da / Density % sol: 55.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 3350, NaCl, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 10, 2003 / Details: mirrors |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→50 Å / Num. all: 46008 / Num. obs: 46008 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 31.2 Å2 / Rsym value: 0.045 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.77→1.82 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3 / Num. unique all: 4536 / Rsym value: 0.312 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1U4H Resolution: 1.77→29.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 849353.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.3006 Å2 / ksol: 0.393477 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.77→29.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.81 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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