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Yorodumi- PDB-1c3a: CRYSTAL STRUCTURE OF FLAVOCETIN-A FROM THE HABU SNAKE VENOM, A NO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c3a | ||||||
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Title | CRYSTAL STRUCTURE OF FLAVOCETIN-A FROM THE HABU SNAKE VENOM, A NOVEL CYCLIC TETRAMER OF C-TYPE LECTIN-LIKE HETERODIMERS | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / C-TYPE LECTIN-LIKE DOMAINS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Trimeresurus flavoviridis (habu) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Fukuda, K. / Mizuno, H. / Atoda, H. / Morita, T. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Crystal structure of flavocetin-A, a platelet glycoprotein Ib-binding protein, reveals a novel cyclic tetramer of C-type lectin-like heterodimers. Authors: Fukuda, K. / Mizuno, H. / Atoda, H. / Morita, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c3a.cif.gz | 62 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c3a.ent.gz | 49.9 KB | Display | PDB format |
PDBx/mmJSON format | 1c3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/1c3a ftp://data.pdbj.org/pub/pdb/validation_reports/c3/1c3a | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a tetramer made up of four identical heterodimers related by a crystallographic fourfold symmetry parallel to the c-axis. |
-Components
#1: Protein | Mass: 15667.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TRIMERESURUS FLAVOVIRIDIS / Source: (natural) Trimeresurus flavoviridis (habu) / References: UniProt: Q8AV97 |
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#2: Protein | Mass: 14563.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TRIMERESURUS FLAVOVIRIDIS / Source: (natural) Trimeresurus flavoviridis (habu) / References: UniProt: Q8AV98 |
#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: 3.77 Å3/Da / Density % sol: 67.4 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 2-methyl-2,4-pentanediol, calcium chloride, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 67 % | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Mar 19, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→85 Å / Num. all: 15775 / Num. obs: 15078 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.5→2.61 Å / Rmerge(I) obs: 0.377 / Num. unique all: 1467 / % possible all: 74.2 |
Reflection shell | *PLUS % possible obs: 74.2 % / Rmerge(I) obs: 0.38 |
-Processing
Software |
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Refinement | Resolution: 2.5→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.6 Å / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.21 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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