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- PDB-1qyy: Crystal Structure of N-Terminal Domain of Human Platelet Receptor... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qyy | |||||||||
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Title | Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-alpha at 2.8 Angstrom Resolution | |||||||||
![]() | Platelet glycoprotein Ib alpha chain | |||||||||
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Function / homology | ![]() thrombin-activated receptor activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Varughese, K.I. / Ruggeri, Z.M. / Celikel, R. | |||||||||
![]() | ![]() Title: Platinum-induced space-group transformation in crystals of the platelet glycoprotein Ib alpha N-terminal domain. Authors: Varughese, K.I. / Ruggeri, Z.M. / Celikel, R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.5 KB | Display | ![]() |
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PDB format | ![]() | 85.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | Chain A or Chain G represent the Biological unit. |
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Components
#1: Protein | Mass: 32306.787 Da / Num. of mol.: 2 / Fragment: N-Terminal Domain / Mutation: C65A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ![]() Source method: isolated from a genetically manipulated source #3: Chemical | #4: Sugar | ChemComp-NAG / | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.63 % | ||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 6000, SODIUM NITRATE, SODIUM ACETATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 31, 2002 | |||||||||
Radiation | Monochromator: 2-Crystal Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→50 Å / Num. all: 16932 / Num. obs: 16932 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rsym value: 0.069 / Net I/σ(I): 8.7 | |||||||||
Reflection shell | Resolution: 2.7→2.85 Å / Mean I/σ(I) obs: 2.2 / Num. unique all: 1163 / Rsym value: 0.317 / % possible all: 72.2 | |||||||||
Reflection | *PLUS Highest resolution: 2.7 Å / Num. measured all: 118489 / Rmerge(I) obs: 0.07 | |||||||||
Reflection shell | *PLUS Highest resolution: 2.7 Å / % possible obs: 72.2 % / Num. unique obs: 1889 / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 2.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: Ab initio Resolution: 2.8→15 Å / Cross valid method: R free / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rfree![]() ![]() | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.377 / Rfactor Rwork: 0.318 |