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Open data
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Basic information
Entry | Database: PDB / ID: 1lml | ||||||
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Title | LEISHMANOLYSIN | ||||||
![]() | LEISHMANOLYSIN | ||||||
![]() | LEISHMANOLYSIN / METALLOPROTEASE / GLYCOPROTEIN | ||||||
Function / homology | ![]() leishmanolysin / : / : / symbiont-mediated perturbation of host inflammatory response / : / metalloendopeptidase activity / metallopeptidase activity / cell adhesion / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schlagenhauf, E. / Etges, R. / Metcalf, P. | ||||||
![]() | ![]() Title: The crystal structure of the Leishmania major surface proteinase leishmanolysin (gp63). Authors: Schlagenhauf, E. / Etges, R. / Metcalf, P. #1: ![]() Title: X-Ray Crystallographic Studies of Leishmanolysin the Leishmania Major Surface Metalloproteinase from Leishmania Major Authors: Schlagenhauf, E. #2: ![]() Title: Crystallization and Preliminary X-Ray Diffraction Studies of Leishmanolysin, the Major Surface Metalloproteinase from Leishmania Major Authors: Schlagenhauf, E. / Etges, R. / Metcalf, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.3 KB | Display | ![]() |
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PDB format | ![]() | 80.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.4 KB | Display | ![]() |
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Full document | ![]() | 430.9 KB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 28.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 51607.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 59.65 % | ||||||||||||||||||||
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Crystal grow | Method: vapor diffusion - hanging drop -macroseeding / pH: 9.5 Details: 52% MPD (2-METHYL-2,4-PENTANEDIOL) 0.1M ETHANOLAMINE-HCL PH 9.5 0.02% NA-AZIDE VAPOR DIFFUSION HANGING DROP METHOD WITH MACROSEEDING, vapor diffusion - hanging drop -macroseeding | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 5.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 278 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 24, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→40 Å / Num. obs: 51879 / % possible obs: 99.7 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.86→1.94 Å / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 3.2 / % possible all: 99.3 |
Reflection | *PLUS % possible obs: 99.5 % / Redundancy: 5.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Resolution: 1.86→5 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: UNINTERPRETABLE WEAK ELECTRON DENSITY WAS OBSERVED FOR RESIDUES 408 - 412, 499 - 504, 575 - 577 AND FOR THE CARBOHYDRATE CHAINS ATTACHED TO N 300, N 407, N 534, N 577.
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Displacement parameters | Biso mean: 24.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.86→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.97 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.195 / Rfactor Rfree: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.94 Å / Rfactor Rfree: 0.272 / % reflection Rfree: 10 % / Rfactor obs: 0.258 |