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Yorodumi- PDB-1ywa: 0.9 A Structure of NP4 from Rhodnius Prolixus complexed with CO a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ywa | ||||||
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Title | 0.9 A Structure of NP4 from Rhodnius Prolixus complexed with CO at pH 5.6 | ||||||
Components | nitrophorin 4 | ||||||
Keywords | LIGAND BINDING PROTEIN / BLOOD CLOTTING / ferrous heme / carbon monoxide complex / lipocalin fold / beta barrel | ||||||
Function / homology | Function and homology information nitrite dismutase / histamine binding / nitric oxide binding / vasodilation / oxidoreductase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodnius prolixus (insect) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.89 Å | ||||||
Authors | Maes, E.M. / Weichsel, A. / Roberts, S.A. / Montfort, W.R. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Ultrahigh Resolution Structures of Nitrophorin 4: Heme Distortion in Ferrous CO and NO Complexes Authors: Maes, E.M. / Roberts, S.A. / Weichsel, A. / Montfort, W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ywa.cif.gz | 111.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ywa.ent.gz | 84.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ywa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ywa_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1ywa_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1ywa_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 1ywa_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/1ywa ftp://data.pdbj.org/pub/pdb/validation_reports/yw/1ywa | HTTPS FTP |
-Related structure data
Related structure data | 1ywbC 1ywcC 1ywdC 1koiS C: citing same article (ref.) 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20292.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodnius prolixus (insect) / Plasmid: PET17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q94734 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-CMO / | #5: 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: 1.94 Å3/Da / Density % sol: 36.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 2.8 M ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 30, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 0.89→19 Å / Num. all: 107559 / Num. obs: 107559 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.038 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 0.89→0.92 Å / Mean I/σ(I) obs: 3.6 / Rsym value: 0.199 / % possible all: 70 |
-Processing
Software |
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Refinement | Starting model: PDB ID 1KOI Resolution: 0.89→10 Å Isotropic thermal model: individual anisotropic temperature factors Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 0.89→10 Å
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Refine LS restraints |
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