+Open data
-Basic information
Entry | Database: PDB / ID: 1l9l | ||||||
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Title | GRANULYSIN FROM HUMAN CYTOLYTIC T LYMPHOCYTES | ||||||
Components | Granulysin | ||||||
Keywords | ANTIMICROBIAL PROTEIN / GRANULYSIN / SAPOSIN FOLD / MEMBRANE-LYTIC | ||||||
Function / homology | Function and homology information phagocytic vesicle lumen / antimicrobial humoral response / Antimicrobial peptides / defense response to fungus / cellular defense response / antimicrobial humoral immune response mediated by antimicrobial peptide / killing of cells of another organism / defense response to bacterium / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 0.92 Å | ||||||
Authors | Anderson, D.H. / Sawaya, M.R. / Cascio, D. / Ernst, W. / Krensky, A. / Modlin, R. / Eisenberg, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Granulysin Crystal Structure and a Structure-Derived Lytic Mechanism Authors: Anderson, D.H. / Sawaya, M.R. / Cascio, D. / Ernst, W. / Modlin, R. / Krensky, A. / Eisenberg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l9l.cif.gz | 62.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l9l.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 1l9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/1l9l ftp://data.pdbj.org/pub/pdb/validation_reports/l9/1l9l | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8679.092 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: LYMPHOCYTE / Plasmid: pET28a (Novagen) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P22749 | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MPO / | #4: Chemical | #5: 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: 1.55 Å3/Da / Density % sol: 20.6 % Description: SE-MET PATTERSON PEAKS WERE 10 SIGMA. PHASING FROM 2 SITES, PLUS INPUT OF SEQUENCE WAS ENOUGH FOR ARP/WARP TO AUTO-BUILD ALMOST THE ENTIRE STRUCTURE. | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 3.1-3.2 M AMMONIUM SULFATE, 0.05 M N-MORPHOLINO PROPANESULFONIC ACID TITRATED TO PH 7 WITH SODIUM HYDROXIDE, 2.5% ETHANOL., VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21-22 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 10, 2002 / Details: PARABOLIC COLLIMATING MIR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 0.92→23.6 Å / Num. all: 35664 / Num. obs: 35664 / % possible obs: 82.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 48.3 |
Reflection shell | Resolution: 0.92→0.96 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1368 / % possible all: 31.7 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 31.7 % / Rmerge(I) obs: 0.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 0.92→23.59 Å / Num. parameters: 7094 / Num. restraintsaints: 9130 / Cross valid method: FREE R / σ(F): 0 / σ(I): -3 StereochEM target val spec case: SULFATE AND ETHANOL COORDINATES WERE OBTAINED FROM CAMBRIDGE CRYSTAL STRUCTURE DATABASE, AND USED AS TARGETS. N-MORPHOLINO PROPANESULFONATE COORDINATES WERE OBTAINED ...StereochEM target val spec case: SULFATE AND ETHANOL COORDINATES WERE OBTAINED FROM CAMBRIDGE CRYSTAL STRUCTURE DATABASE, AND USED AS TARGETS. N-MORPHOLINO PROPANESULFONATE COORDINATES WERE OBTAINED FROM HIC-UP AND SYMMETRIZED FOR TARGET VALUES Stereochemistry target values: ENGH & HUBER Details: WATER MOLECULES WITH APPARENT COLLISIONS: NOT ALL WATERS IN THE MODEL CAN BE PRESENT SIMULTANEOUSLY. HOH 1021 IN POSITIONS A AND B CORRESPONDS TO ASP 72 IN CONFORMATIONS A AND B, ...Details: WATER MOLECULES WITH APPARENT COLLISIONS: NOT ALL WATERS IN THE MODEL CAN BE PRESENT SIMULTANEOUSLY. HOH 1021 IN POSITIONS A AND B CORRESPONDS TO ASP 72 IN CONFORMATIONS A AND B, RESPECTIVELY. HOH 1041 IN POSITIONS A AND B CORRESPONDS TO GLN 12 IN CONFORMATIONS A AND B, RESPECTIVELY. HOH 1080 IN POSITION B CORRESPONDS TO ASP 43 IN CONFORMATION B; IT WOULD COLLIDE WITH CONFORMATION A. GLN 12 AND ASP 72 OF A SYMMETRY-RELATED MOLECULE CAN SIMULTANEOUSLY OCCUPY THEIR CONFORMATIONS A, ALONG WITH HOH 1021A AND 1041A, BUT EITHER SIDE CHAIN IN ITS CONFORMATION A WILL EXCLUDE HOH 1021B.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 13 / Occupancy sum hydrogen: 620.82 / Occupancy sum non hydrogen: 727.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.92→23.59 Å
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Refine LS restraints |
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LS refinement shell |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rwork: 0.138 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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