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Yorodumi- PDB-1shu: Crystal Structure of the von Willebrand factor A domain of human ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1shu | ||||||
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Title | Crystal Structure of the von Willebrand factor A domain of human capillary morphogenesis protein 2: an anthrax toxin receptor | ||||||
Components | Anthrax toxin receptor 2 | ||||||
Keywords | MEMBRANE PROTEIN / alpha/beta Rossmann fold | ||||||
Function / homology | Function and homology information Uptake and function of anthrax toxins / transmembrane signaling receptor activity / endosome membrane / endoplasmic reticulum membrane / cell surface / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Lacy, D.B. / Wigelsworth, D.J. / Scobie, H.M. / Young, J.A.T. / Collier, R.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Crystal Structure of the von Willebrand factor A domain of human capillary morphogenesis protein 2: an anthrax toxin receptor Authors: Lacy, D.B. / Wigelsworth, D.J. / Scobie, H.M. / Young, J.A.T. / Collier, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1shu.cif.gz | 88.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1shu.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 1shu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1shu_validation.pdf.gz | 423.5 KB | Display | wwPDB validaton report |
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Full document | 1shu_full_validation.pdf.gz | 424.5 KB | Display | |
Data in XML | 1shu_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 1shu_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/1shu ftp://data.pdbj.org/pub/pdb/validation_reports/sh/1shu | HTTPS FTP |
-Related structure data
Related structure data | 1shtSC S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 19897.842 Da / Num. of mol.: 1 / Fragment: VWA domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANTXR2, CMG2 / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21.DE3 / References: UniProt: P58335 |
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#2: Chemical | ChemComp-MG / |
#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: 2.35 Å3/Da / Density % sol: 47.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG3350, magnesium chloride, bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9186 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 17, 2003 |
Radiation | Monochromator: horizontally bent, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9186 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→28.75 Å / Num. all: 30193 / Num. obs: 30193 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 33.3 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 7.7 / Num. unique all: 2728 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SHT Resolution: 1.5→28.75 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.262 / SU ML: 0.049 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.077 / 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: 16.871 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→28.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0.077 / Total num. of bins used: 20
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