[English] 日本語
Yorodumi
- PDB-1l9l: GRANULYSIN FROM HUMAN CYTOLYTIC T LYMPHOCYTES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1l9l
TitleGRANULYSIN FROM HUMAN CYTOLYTIC T LYMPHOCYTES
ComponentsGranulysinGNLY
KeywordsANTIMICROBIAL 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
Granulysin-like / Saposin-like / NK-Lysin / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

#1: Protein Granulysin / GNLY / 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 / Sulfate


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


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


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


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more