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- PDB-1l9l: GRANULYSIN FROM HUMAN CYTOLYTIC T LYMPHOCYTES -

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Basic information

Entry
Database: PDB / ID: 1l9l
TitleGRANULYSIN FROM HUMAN CYTOLYTIC T LYMPHOCYTES
ComponentsGranulysin
KeywordsANTIMICROBIAL PROTEIN / GRANULYSIN / SAPOSIN FOLD / MEMBRANE-LYTIC
Function / homology
Function and homology information


phagocytic vesicle lumen / 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
Granulysin-like / Saposin-like / NK-Lysin / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin (B) Domains / Saposin B type domain / Saposin-like / Saposin B type domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ETHANOL / Granulysin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 0.92 Å
AuthorsAnderson, D.H. / Sawaya, M.R. / Cascio, D. / Ernst, W. / Krensky, A. / Modlin, R. / Eisenberg, D.
CitationJournal: 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
DepositionMar 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 13, 2017Group: Refinement description / Category: refine / Item: _refine.pdbx_method_to_determine_struct
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Granulysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4119
Polymers8,6791
Non-polymers7328
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.265, 60.436, 23.591
Angle α, β, γ (deg.)90.00, 90.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Granulysin / T-cell activation protein 519 / NKG5 protein / Lymphokine LAG-2


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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity 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.
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
23.1-3.2 Mammonium sulfate1reservoir
30.05 Msodium MOPS1reservoirpH7.
42.5 %(v/v)ethanol1reservoir
53.2 Mammonium sulfate1drop
60.05 Msodium MOPS1drop
72.5 %(v/v)ethanol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 10, 2002 / Details: PARABOLIC COLLIMATING MIR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
SHELXL-97refinement
DMphasing
RefinementMethod 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.1898 1812 5 %RANDOM
Rwork0.137 ---
obs0.138 33317 79.2 %-
all-35633 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 13 / Occupancy sum hydrogen: 620.82 / Occupancy sum non hydrogen: 727.7
Refinement stepCycle: LAST / Resolution: 0.92→23.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1331 0 33 104 1468
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.038
X-RAY DIFFRACTIONs_similar_dist0.014
X-RAY DIFFRACTIONs_from_restr_planes0.024
X-RAY DIFFRACTIONs_zero_chiral_vol0.083
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.108
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.076
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.052
X-RAY DIFFRACTIONs_approx_iso_adps0.075
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
0.92-10.19X-RAY DIFFRACTION363710
1-1.050.141X-RAY DIFFRACTION354810
1.05-1.10.124X-RAY DIFFRACTION361610
1.1-1.160.115X-RAY DIFFRACTION347010
1.16-1.230.11X-RAY DIFFRACTION353710
1.23-1.330.108X-RAY DIFFRACTION357510
1.33-1.470.11X-RAY DIFFRACTION355710
1.47-1.690.113X-RAY DIFFRACTION358510
1.69-2.120.124X-RAY DIFFRACTION351310
2.12-300.17X-RAY DIFFRACTION359510
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
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_planar_d0.024
X-RAY DIFFRACTIONs_plane_restr0.083

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