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- PDB-20gs: GLUTATHIONE S-TRANSFERASE P1-1 COMPLEXED WITH CIBACRON BLUE -

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Basic information

Entry
Database: PDB / ID: 20gs
TitleGLUTATHIONE S-TRANSFERASE P1-1 COMPLEXED WITH CIBACRON BLUE
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / GLUTATHIONE TRANSFERASE / LIGAND / CIBACRON BLUE / DETOXIFICATION
Function / homology
Function and homology information


S-nitrosoglutathione binding / nitric oxide storage / negative regulation of leukocyte proliferation / TRAF2-GSTP1 complex / negative regulation of smooth muscle cell chemotaxis / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / cellular response to cell-matrix adhesion / hepoxilin biosynthetic process / glutathione derivative biosynthetic process ...S-nitrosoglutathione binding / nitric oxide storage / negative regulation of leukocyte proliferation / TRAF2-GSTP1 complex / negative regulation of smooth muscle cell chemotaxis / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / cellular response to cell-matrix adhesion / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / response to L-ascorbic acid / linoleic acid metabolic process / Glutathione conjugation / nitric oxide binding / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / glutathione peroxidase activity / Paracetamol ADME / oligodendrocyte development / negative regulation of stress-activated MAPK cascade / negative regulation of JNK cascade / prostaglandin metabolic process / cellular response to glucocorticoid stimulus / negative regulation of interleukin-1 beta production / regulation of stress-activated MAPK cascade / Detoxification of Reactive Oxygen Species / negative regulation of acute inflammatory response / glutathione transferase / negative regulation of vascular associated smooth muscle cell proliferation / glutathione transferase activity / protein serine/threonine kinase inhibitor activity / negative regulation of tumor necrosis factor production / animal organ regeneration / negative regulation of tumor necrosis factor-mediated signaling pathway / response to amino acid / toxic substance binding / regulation of ERK1 and ERK2 cascade / negative regulation of fibroblast proliferation / negative regulation of MAPK cascade / positive regulation of superoxide anion generation / negative regulation of canonical NF-kappaB signal transduction / glutathione metabolic process / xenobiotic metabolic process / cellular response to epidermal growth factor stimulus / fatty acid binding / central nervous system development / response to reactive oxygen species / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of ERK1 and ERK2 cascade / cellular response to insulin stimulus / response to estradiol / cellular response to lipopolysaccharide / response to ethanol / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / Neutrophil degranulation / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / mitochondrion / extracellular space / extracellular exosome / extracellular region / nucleus / cytoplasm / cytosol
Similarity search - Function
Glutathione S-transferase, Pi class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Glutathione S-transferase, Pi class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-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
CIBACRON BLUE / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsOakley, A.J. / Lo Bello, M. / Nuccetelli, M. / Mazzetti, A.P. / Parker, M.W.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: The ligandin (non-substrate) binding site of human Pi class glutathione transferase is located in the electrophile binding site (H-site).
Authors: Oakley, A.J. / Lo Bello, M. / Nuccetelli, M. / Mazzetti, A.P. / Parker, M.W.
#1: Journal: J.Mol.Biol. / Year: 1997
Title: The Structures of Human Glutathione Transferase P1-1 in Complex with Glutathione and Various Inhibitors at High Resolution
Authors: Oakley, A.J. / Lo Bello, M. / Battistoni, A. / Ricci, G. / Rossjohn, J. / Villar, H.O. / Parker, M.W.
History
DepositionDec 16, 1997Processing site: BNL
Revision 1.0Dec 30, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4326
Polymers46,4932
Non-polymers1,9394
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-11 kcal/mol
Surface area17920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.176, 90.690, 68.755
Angle α, β, γ (deg.)90.00, 97.73, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.943003, 0.116095, 0.311878), (0.115164, -0.993114, 0.021468), (0.312223, 0.015672, -0.94988)
Vector: -5.6823, 21.52458, 27.31725)

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE / GSTP1-1


Mass: 23246.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: UBIQUITOUS / Cell: UBIQUITOUS / Cellular location: CYTOSOL / Gene: GSTP1 / Organ: UBIQUITOUS / Gene (production host): GSTP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09211, glutathione transferase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


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


Mass: 774.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H20ClN7O11S3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsNOT ALL OF THE LIGAND CIBACRON BLUE WAS SEEN IN DENSITY. THEREFORE, ONLY A PORTION OF THE MOLECULE ...NOT ALL OF THE LIGAND CIBACRON BLUE WAS SEEN IN DENSITY. THEREFORE, ONLY A PORTION OF THE MOLECULE IS INCLUDED IN THIS ENTRY.

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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: 2.6 Å3/Da / Density % sol: 52.62 %
Crystal growMethod: vapor diffusion - hanging drop - streak seeding / pH: 6
Details: CRYSTALLISATION PERFORMED USING THE HANGING DROP TECHNIQUE. 2 MICROL OF PROTEIN SOLUTION (8MG/ML) IN 10MM PHOSPHATE BUFFER PH7.0, 1MM EDTA AND 2MM BETA-MERCAPTOETHANOL WAS ADDED TO 2 MICROL ...Details: CRYSTALLISATION PERFORMED USING THE HANGING DROP TECHNIQUE. 2 MICROL OF PROTEIN SOLUTION (8MG/ML) IN 10MM PHOSPHATE BUFFER PH7.0, 1MM EDTA AND 2MM BETA-MERCAPTOETHANOL WAS ADDED TO 2 MICROL OF RESERVOIR SOLUTION. THE RESERVOIR CONTAINED 20-25% AMMONIUM SULFATE, 30-60 MM DITHIOTHREITOL AND 100MM MORPHOLINOETHANESULFONIC ACID BUFFER PH5.4. DROPS WERE STREAK SEEDED AFTER 1 DAY USING A CAT'S WHISKER FROM CRYSTALS GROWN UNDER SIMILAR CONDITIONS. SOLID CIBACRON BLUE WAS SEEDED INTO THE DROP. SIX WEEKS LATER THE CRYSTALS WERE SUBJECTED TO X-RAY ANALYSIS., pH 6.0, vapor diffusion - hanging drop - streak seeding
PH range: 5.4-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 31, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→15 Å / Num. obs: 16729 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 2.97 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 9.2
Reflection shellResolution: 2.45→2.54 Å / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 2.7 / % possible all: 93.9

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5GSS

5gss


Resolution: 2.45→15 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.28 817 4.9 %RANDOM
Rwork0.229 ---
obs0.229 16727 95.8 %-
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1-8.17 Å20 Å2-2.02 Å2
2--0.07 Å20 Å2
3----8.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.31 Å
Luzzati d res low-15 Å
Luzzati sigma a0.4 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.45→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 0 169 101 3532
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.67
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.541.5
X-RAY DIFFRACTIONx_mcangle_it2.362
X-RAY DIFFRACTIONx_scbond_it2.452
X-RAY DIFFRACTIONx_scangle_it3.392.5
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 2.45→2.54 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.416 90 5.6 %
Rwork0.293 1524 -
obs--93.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2MES.PARMES.TOP
X-RAY DIFFRACTION3CBD.PARCBD.TOP
X-RAY DIFFRACTION4WATER.PROWATER.TOP

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