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Yorodumi- PDB-1u18: 1.96 A Crystal structure of H60C mutant of nitrophorin complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u18 | ||||||
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Title | 1.96 A Crystal structure of H60C mutant of nitrophorin complexed with histamine | ||||||
Components | Nitrophorin 1 | ||||||
Keywords | SIGNALING PROTEIN / lipocalin / beta barrel / ferric heme | ||||||
Function / homology | Function and homology information histamine binding / nitric oxide binding / vasodilation / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodnius prolixus (insect) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Vetter, S.W. / Goodin, D.B. | ||||||
Citation | Journal: TO BE PUBLISHED Title: 1.96 A Crystal structure of H60C mutant of nitrophorin complexed with histamine Authors: Vetter, S.W. / Goodin, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u18.cif.gz | 91.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u18.ent.gz | 70 KB | Display | PDB format |
PDBx/mmJSON format | 1u18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/1u18 ftp://data.pdbj.org/pub/pdb/validation_reports/u1/1u18 | HTTPS FTP |
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-Related structure data
Related structure data | 2np1S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20607.059 Da / Num. of mol.: 2 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): BL21(DE3) / References: UniProt: Q26239 #2: Chemical | #3: Chemical | #4: Chemical | #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: 2.25 Å3/Da / Density % sol: 45.3 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M potassium cacodylate, 2.9 M di-ammonium hydrogen phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 24, 2003 / Details: osmic confocal mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→27 Å / Num. all: 26246 / Num. obs: 22695 / % possible obs: 92 % / Redundancy: 2.1 % / Rsym value: 0.038 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.96→2.06 Å / Redundancy: 1.08 % / Rmerge(I) obs: 0.038 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3724 / Rsym value: 0.0125 / % possible all: 70.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 2NP1 Resolution: 1.96→27 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.785 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.658 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.011 Å / Total num. of bins used: 20 /
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