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- PDB-1lbk: Crystal structure of a recombinant glutathione transferase, creat... -

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Basic information

Entry
Database: PDB / ID: 1lbk
TitleCrystal structure of a recombinant glutathione transferase, created by replacing the last seven residues of each subunit of the human class pi isoenzyme with the additional C-terminal helix of human class alpha isoenzyme
ComponentsGlutathione S-transferase class pi chimaera (CODA)
KeywordsTRANSFERASE / Glutathione Transferase P1-1 / Chimaera / Recombinant Protein / Substrate Specificity
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / nitric oxide storage / S-nitrosoglutathione binding / kinase regulator activity / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process ...Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / nitric oxide storage / S-nitrosoglutathione binding / kinase regulator activity / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / negative regulation of JUN kinase activity / steroid delta-isomerase activity / nitric oxide binding / linoleic acid metabolic process / negative regulation of leukocyte proliferation / Glutathione conjugation / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / Paracetamol ADME / glutathione peroxidase activity / Azathioprine ADME / negative regulation of stress-activated MAPK cascade / Heme degradation / negative regulation of interleukin-1 beta production / NFE2L2 regulating anti-oxidant/detoxification enzymes / regulation of stress-activated MAPK cascade / prostaglandin metabolic process / negative regulation of MAPK cascade / Detoxification of Reactive Oxygen Species / glutathione transferase / negative regulation of acute inflammatory response / glutathione transferase activity / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / glutathione metabolic process / negative regulation of canonical NF-kappaB signal transduction / negative regulation of fibroblast proliferation / epithelial cell differentiation / xenobiotic metabolic process / response to reactive oxygen species / regulation of ERK1 and ERK2 cascade / negative regulation of MAP kinase activity / positive regulation of superoxide anion generation / central nervous system development / fatty acid binding / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / secretory granule lumen / cellular response to lipopolysaccharide / vesicle / ficolin-1-rich granule lumen / Neutrophil degranulation / negative regulation of apoptotic process / mitochondrion / extracellular space / extracellular exosome / extracellular region / nucleus / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase, alpha class / Glutathione S-transferase, Pi class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. ...Glutathione S-transferase, alpha class / Glutathione S-transferase, Pi class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Glutathione S-transferase A1 / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsKong, G.K.W. / Micaloni, C. / Mazzetti, A.P. / Nuccetelli, M. / Antonini, G. / Stella, L. / McKinstry, W.J. / Polekhina, G. / Rossjohn, J. / Federici, G. ...Kong, G.K.W. / Micaloni, C. / Mazzetti, A.P. / Nuccetelli, M. / Antonini, G. / Stella, L. / McKinstry, W.J. / Polekhina, G. / Rossjohn, J. / Federici, G. / Ricci, G. / Parker, M.W. / Lo Bello, M.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Engineering a new C-terminal tail in the H-site of human glutathione transferase P1-1: structural and functional consequences.
Authors: Micaloni, C. / Kong, G.K.W. / Mazzetti, A.P. / Nuccetelli, M. / Antonini, G. / Stella, L. / McKinstry, W.J. / Polekhina, G. / Rossjohn, J. / Federici, G. / Ricci, G. / Parker, M.W. / Lo Bello, M.
History
DepositionApr 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Glutathione S-transferase class pi chimaera (CODA)
B: Glutathione S-transferase class pi chimaera (CODA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5787
Polymers46,4772
Non-polymers1,1015
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-39 kcal/mol
Surface area17790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.300, 79.300, 89.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutathione S-transferase class pi chimaera (CODA)


Mass: 23238.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN IS A RECOMBINANT GLUTATHIONE TRANSFERASE CREATED BY REPLACING THE LAST SEVEN RESIDUES in each subunit of human glutathione transferase P1-1 WITH RESIDUES 208-213 OF human ...Details: THE PROTEIN IS A RECOMBINANT GLUTATHIONE TRANSFERASE CREATED BY REPLACING THE LAST SEVEN RESIDUES in each subunit of human glutathione transferase P1-1 WITH RESIDUES 208-213 OF human glutathione transferase A1-1.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pse420 / Production host: Escherichia coli (E. coli) / Strain (production host): top 10
References: UniProt: P09211, UniProt: P08263, glutathione transferase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000, calcium chloride, glutathione, (R,R)-1,4-dithiothreitol, 2-[N-morpholino]ethanesulphonic acid, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / PH range low: 6.5 / PH range high: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18.5 mg/mlprotein1drop
210 mMphosphate1droppH7.0
30.1 mMEDTA1drop
420-25 %(w/v)PEG80001reservoir
510 mMdithiothreitol1reservoir
6100 mMMES1reservoirpH5.5-6.5
71 mMGSH1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 2001
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→15 Å / Num. all: 41681 / Num. obs: 41262 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 37.3
Reflection shellResolution: 1.86→1.93 Å / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 6.7 / % possible all: 96.4
Reflection
*PLUS
Num. measured all: 158396
Reflection shell
*PLUS
% possible obs: 96.4 % / Mean I/σ(I) obs: 6.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 7gss

7gss


Resolution: 1.86→14.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1527567.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 4076 9.9 %RANDOM
Rwork0.198 ---
obs0.198 41209 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.7633 Å2 / ksol: 0.428405 e/Å3
Displacement parametersBiso mean: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2--5.54 Å20 Å2
3----4.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.86→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 109 450 3831
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.672
X-RAY DIFFRACTIONc_scbond_it1.932
X-RAY DIFFRACTIONc_scangle_it2.732.5
LS refinement shellResolution: 1.86→1.98 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 607 9.1 %
Rwork0.26 6094 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4GSH.PARGSH.TOP
X-RAY DIFFRACTION5MES.PARMES.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.15
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

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