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Open data
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Basic information
Entry | Database: PDB / ID: 1flh | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN UROPEPSIN AT 2.45 A RESOLUTION | ||||||
![]() | UROPEPSIN | ||||||
![]() | HYDROLASE / ACID PROTEINASE | ||||||
Function / homology | ![]() multivesicular body lumen / pepsin A / Surfactant metabolism / digestion / aspartic-type endopeptidase activity / proteolysis / extracellular exosome Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Canduri, F. / Teodoro, L.G.V.L. / Fadel, V. / Lorenzi, C.C.B. / Hial, V. / Gomes, R.A.S. / Neto, J.R. / De Azevedo Jr., W.F. | ||||||
![]() | ![]() Title: Structure of human uropepsin at 2.45 A resolution. Authors: Canduri, F. / Teodoro, L.G. / Fadel, V. / Lorenzi, C.C. / Hial, V. / Gomes, R.A. / Neto, J.R. / de Azevedo, W.F. #1: ![]() Title: Crystallization, Preliminary X-Ray Analysis and Patterson Search of a New Aspartic Protease Isolate from Human Urine Authors: Canduri, F. / Teodoro, L.G.V.L. / Lorenzi, C.C.B. / Gomes, R.A.S. / Fontes, M.R.M. / Arni, R.K. / De Azevedo Jr., W.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.4 KB | Display | ![]() |
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PDB format | ![]() | 54.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 410.6 KB | Display | ![]() |
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Full document | ![]() | 415.5 KB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1psnS S: Starting model for refinement |
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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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Components
#1: Protein | Mass: 34617.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.3 % | ||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 7 Details: 0.1M HEPES BUFFER (pH 7.0), 2% PEG 400, 2.0M AMMONIUM SULFATE., VAPOR DIFFUSION | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 12, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.38 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→12 Å / Num. obs: 13134 / % possible obs: 98.9 % / Observed criterion σ(I): 1 / Redundancy: 3.26 % / Rmerge(I) obs: 0.077 |
Reflection | *PLUS Num. measured all: 24189 |
Reflection shell | *PLUS Highest resolution: 2.45 Å / Lowest resolution: 2.51 Å / % possible obs: 99.1 % / Rmerge(I) obs: 0.303 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PSN Resolution: 2.45→12 Å / σ(F): 2
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Displacement parameters | Biso mean: 15.52 Å2 | |||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.19 Å | |||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→12 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | |||||||||||||||
Refinement | *PLUS Lowest resolution: 12 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor Rfree: 0.251 | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS
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