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- PDB-5l6x: CRYSTAL STRUCTURE OF HGSTP1-1 COMPLEXED WITH FERROCENE-GLUTATHION... -

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Basic information

Entry
Database: PDB / ID: 5l6x
TitleCRYSTAL STRUCTURE OF HGSTP1-1 COMPLEXED WITH FERROCENE-GLUTATHIONE CONJUGATE
ComponentsGlutathione S-transferase P
KeywordsTRANSFERASE / glutathione S-transferases / Ferrocene-glutathione conjugate / inhibitor complex / detoxification
Function / homology
Function and homology information


S-nitrosoglutathione binding / nitric oxide storage / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / kinase regulator activity / negative regulation of leukocyte proliferation / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / glutathione derivative biosynthetic process / hepoxilin biosynthetic process ...S-nitrosoglutathione binding / nitric oxide storage / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / kinase regulator activity / negative regulation of leukocyte proliferation / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / glutathione derivative biosynthetic process / hepoxilin biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / negative regulation of JUN kinase activity / nitric oxide binding / linoleic acid metabolic process / Glutathione conjugation / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / Paracetamol ADME / glutathione peroxidase activity / negative regulation of stress-activated MAPK cascade / negative regulation of interleukin-1 beta production / negative regulation of MAPK cascade / regulation of stress-activated MAPK cascade / prostaglandin metabolic process / Detoxification of Reactive Oxygen Species / negative regulation of acute inflammatory response / glutathione transferase / negative regulation of tumor necrosis factor production / glutathione transferase activity / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of fibroblast proliferation / negative regulation of canonical NF-kappaB signal transduction / glutathione metabolic process / xenobiotic metabolic process / regulation of ERK1 and ERK2 cascade / positive regulation of superoxide anion generation / negative regulation of MAP kinase activity / central nervous system development / fatty acid binding / response to reactive oxygen species / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / cellular response to lipopolysaccharide / secretory granule lumen / 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, 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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like ...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 / 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
Chem-6SG / AZIDE ION / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsLopez-Jaramillo, F.J. / Garcia-Fuentes, L. / Vargas-Berenguel, A.
Funding support Spain, 3items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessCTQ2013-48380-R Spain
Marie Sklodowska-Curie ITN programCYCLON Hit 608407
Spanish Ministry of Economy and CompetitivenessCTQ2014-55474-C2-1-R Spain
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF HGSTP1-1 COMPLEXED WITH FERROCENE-GLUTATHIONE CONJUGATE
Authors: Lopez-Jaramillo, F.J. / Vargas-Berenguel, A. / Garcia-Fuentes, L.
History
DepositionJun 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Nov 6, 2019Group: Atomic model / Data collection / Category: atom_site / diffrn_detector / Item: _atom_site.occupancy / _diffrn_detector.detector
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase P
B: Glutathione S-transferase P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,27415
Polymers46,7032
Non-polymers1,57113
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-13 kcal/mol
Surface area17410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.023, 89.410, 68.604
Angle α, β, γ (deg.)90.000, 97.816, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-448-

HOH

21B-583-

HOH

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Components

#1: Protein Glutathione S-transferase P / GST class-pi / GSTP1-1


Mass: 23351.732 Da / Num. of mol.: 2 / Mutation: P2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTP1, FAEES3, GST3 / Production host: Escherichia coli (E. coli) / References: UniProt: P09211, glutathione transferase
#2: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: N3
#3: Chemical ChemComp-6SG / S-[N-(ferrocenylmethyl)carbamoylmethyl]-glutathione


Mass: 554.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H22FeN4O7S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM HEPES pH 6, 10 mM DTT, 100 mM CaCl2, 30% PEG 6000, Ligand was soaked o/n prior diffraction

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryo
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Aug 20, 2013 / Details: Helios
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.995→19 Å / Num. obs: 31283 / % possible obs: 99.04 % / Redundancy: 5.79 % / Rsym value: 0.07 / Net I/av σ(I): 78.604 / Net I/σ(I): 31.148 / Num. measured all: 181113
Reflection shell
Resolution (Å)Highest resolution (Å)Rsym valueDiffraction-IDRejects
1.995-2.0660.18710
2.066-2.1490.15710
2.149-2.2470.12710
2.247-2.3650.11310
2.365-2.5130.110
2.513-2.7070.09310
2.707-2.9790.08210
2.979-3.4080.06710
3.408-4.2880.05710
4.2880.05210

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Processing

Software
NameVersionClassification
CNSrefinement
SAINTV8.30Cdata scaling
PDB_EXTRACT3.2data extraction
SAINTV8.30Cdata reduction
CNS1.2phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3pgt

3pgt


Resolution: 2→10 Å / FOM work R set: 0.8778 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 3016 9.8 %Random
Rwork0.1806 27673 --
obs-30689 99.3 %-
Solvent computationBsol: 70.1026 Å2
Displacement parametersBiso max: 51.36 Å2 / Biso mean: 11.5663 Å2 / Biso min: 1.25 Å2
Baniso -1Baniso -2Baniso -3
1-2.812 Å20 Å2-1.589 Å2
2---1.125 Å20 Å2
3----1.687 Å2
Refinement stepCycle: final / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3275 0 490 0 3765
Biso mean--16.39 --
Num. residues----419
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d1.546
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.010.3126610.2198515576
2.01-2.030.3083550.2283531586
2.03-2.040.2505590.2169518577
2.04-2.060.2667570.2199533590
2.06-2.070.2551500.1922554604
2.07-2.090.2443600.2004577637
2.09-2.10.2449630.2052543606
2.1-2.120.2362530.1943538591
2.12-2.140.2073610.1822559620
2.14-2.150.2462550.1919558613
2.15-2.170.2105600.1983537597
2.17-2.190.2527530.1851583636
2.19-2.210.2149640.1733525589
2.21-2.230.209600.184550610
2.23-2.250.2551450.1849578623
2.25-2.270.2418520.1744565617
2.27-2.290.2246730.1772544617
2.29-2.320.2086710.1801523594
2.32-2.340.2677630.1893571634
2.34-2.370.2088530.1762560613
2.37-2.390.2586670.1754541608
2.39-2.420.2295460.1641554600
2.42-2.450.236470.1834593640
2.45-2.480.2104680.1555545613
2.48-2.510.2439500.1741538588
2.51-2.550.2154620.1843581643
2.55-2.580.2097580.1766546604
2.58-2.620.2402630.1943571634
2.62-2.660.2165680.1799528596
2.66-2.70.2275740.1885545619
2.7-2.750.2355630.1854553616
2.75-2.80.2668680.2019553621
2.8-2.850.207700.1844539609
2.85-2.910.316610.2071565626
2.91-2.970.211580.1971575633
2.97-3.040.1826510.1677544595
3.04-3.110.2243710.1997558629
3.11-3.190.2095580.2004550608
3.19-3.280.2257610.1843566627
3.28-3.380.1837610.1977533594
3.38-3.50.2181570.1806582639
3.5-3.630.226700.1849563633
3.63-3.790.182480.1659552600
3.79-3.980.172630.16562625
3.98-4.210.1375560.1396573629
4.21-4.510.1171640.1397557621
4.51-4.910.1695570.1555568625
4.91-5.520.1534660.1583553619
5.52-6.60.1911740.1724558632
6.6-100.1889680.1808565633
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4ligand.par

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