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Open data
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Basic information
Entry | Database: PDB / ID: 1pu4 | |||||||||
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Title | Crystal structure of human vascular adhesion protein-1 | |||||||||
![]() | Membrane copper amine oxidase | |||||||||
![]() | OXIDOREDUCTASE / amine oxidase | |||||||||
Function / homology | ![]() primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / Phase I - Functionalization of compounds / microvillus / quinone binding / early endosome / cell adhesion / inflammatory response ...primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / Phase I - Functionalization of compounds / microvillus / quinone binding / early endosome / cell adhesion / inflammatory response / copper ion binding / protein heterodimerization activity / response to antibiotic / calcium ion binding / Golgi apparatus / cell surface / endoplasmic reticulum / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Salminen, T.A. / Airenne, T.T. | |||||||||
![]() | ![]() Title: Crystal structure of the human vascular adhesion protein-1: unique structural features with functional implications. Authors: Airenne, T.T. / Nymalm, Y. / Kidron, H. / Smith, D.J. / Pihlavisto, M. / Salmi, M. / Jalkanen, S. / Johnson, M.S. / Salminen, T.A. #1: ![]() Title: Crystallization and preliminary X-ray analysis of the human vascular adhesion protein-1 Authors: Nymalm, Y. / Kidron, H. / Soderholm, A. / Viitanen, L. / Kaukonen, K. / Pihlavisto, M. / Smith, D. / Veromaa, T. / Airenne, T.T. / Johnson, M.S. / Salminen, T.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 283.5 KB | Display | ![]() |
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PDB format | ![]() | 228.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 52 KB | Display | |
Data in CIF | ![]() | 69.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1us1C ![]() 1ksiS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 84734.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | #4: Chemical | #5: Chemical | ChemComp-CA / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.75 Å3/Da / Density % sol: 74.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: potassium/sodium tartrate, imidazole, sodium chloride, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 5, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.811 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→20 Å / Num. obs: 52367 / % possible obs: 95.9 % / Redundancy: 14.1 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 3.2→3.3 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 6 / Num. unique all: 4588 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KSI Resolution: 3.2→20 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.868 / SU B: 16.555 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 1.054 / ESU R Free: 0.396 / 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: 28.543 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.2→3.281 Å / Total num. of bins used: 20
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