+Open data
-Basic information
Entry | Database: PDB / ID: 1lml | ||||||
---|---|---|---|---|---|---|---|
Title | LEISHMANOLYSIN | ||||||
Components | LEISHMANOLYSIN | ||||||
Keywords | LEISHMANOLYSIN / METALLOPROTEASE / GLYCOPROTEIN | ||||||
Function / homology | Function and homology information leishmanolysin / : / : / symbiont-mediated perturbation of host inflammatory response / : / metalloendopeptidase activity / metallopeptidase activity / cell adhesion / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Leishmania major (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR, MOLECULAR REPLACEMENT USING TWO CRYSTAL FORMS / Resolution: 1.86 Å | ||||||
Authors | Schlagenhauf, E. / Etges, R. / Metcalf, P. | ||||||
Citation | Journal: Structure / Year: 1998 Title: The crystal structure of the Leishmania major surface proteinase leishmanolysin (gp63). Authors: Schlagenhauf, E. / Etges, R. / Metcalf, P. #1: Journal: Thesis Title: X-Ray Crystallographic Studies of Leishmanolysin the Leishmania Major Surface Metalloproteinase from Leishmania Major Authors: Schlagenhauf, E. #2: Journal: Proteins / Year: 1995 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1lml.cif.gz | 101.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1lml.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 1lml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/1lml ftp://data.pdbj.org/pub/pdb/validation_reports/lm/1lml | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 51607.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / Cellular location: MEMBRANE BOUND / Strain: LRC-L119 / References: UniProt: P08148, leishmanolysin |
---|---|
#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 59.65 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 278 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X31 / Wavelength: 0.87 |
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 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR, MOLECULAR REPLACEMENT USING TWO CRYSTAL FORMS 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.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.86→1.97 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.195 / Rfactor Rfree: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Lowest resolution: 1.94 Å / Rfactor Rfree: 0.272 / % reflection Rfree: 10 % / Rfactor obs: 0.258 |