+Open data
-Basic information
Entry | Database: PDB / ID: 1ywd | ||||||
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Title | 1.08 A Structure of Ferrous NP4 (aquo complex) | ||||||
Components | nitrophorin 4 | ||||||
Keywords | LIGAND BINDING PROTEIN / BLOOD CLOTTING / ferrous heme / 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 / starting model 1D2U / Resolution: 1.08 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 | 1ywd.cif.gz | 103 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ywd.ent.gz | 78.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ywd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/1ywd ftp://data.pdbj.org/pub/pdb/validation_reports/yw/1ywd | HTTPS FTP |
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-Related structure data
Related structure data | 1ywaC 1ywbC 1ywcC 1d2uS 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 | ChemComp-HEM / |
#3: 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: 1.93 Å3/Da / Density % sol: 36.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: 2.8 M ammonium phosphate, pH 7.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.751 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 20, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.751 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→30 Å / Num. all: 64299 / Num. obs: 64299 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rsym value: 0.052 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.08→1.12 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2 / Num. unique all: 6266 / Rsym value: 0.228 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: starting model 1D2U Starting model: PDB ID 1D2U Resolution: 1.08→10 Å Isotropic thermal model: individual anisotropic thermal parameters Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.08→10 Å
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Refine LS restraints |
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