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- PDB-6rwd: Crystal structure of SjGST in complex with GSH and ellagic acid a... -

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Basic information

Entry
Database: PDB / ID: 6rwd
TitleCrystal structure of SjGST in complex with GSH and ellagic acid at 1.53 Angstrom resolution
ComponentsGlutathione S-transferase class-mu 26 kDa isozyme
KeywordsTRANSFERASE / Schistosoma japonicum / SjGST / Ellagic Acid / GSH / 1.53Ang
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process
Similarity search - Function
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, 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
GLUTATHIONE / Chem-REF / Glutathione S-transferase class-mu 26 kDa isozyme
Similarity search - Component
Biological speciesSchistosoma japonicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsOlfsen, J. / Pandian, R. / Sayed, Y. / Dirr, H.W. / Achilonu, I.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Science and Technology Funding CouncilST/R002754/1 United Kingdom
CitationJournal: Mol.Biochem.Parasitol. / Year: 2020
Title: Molecular basis of inhibition of Schistosoma japonicum glutathione transferase by ellagic acid: Insights into biophysical and structural studies.
Authors: Akumadu, B.O. / Pandian, R. / Olfsen, J. / Worth, R. / Thulo, M. / Mentor, T. / Fanucchi, S. / Sayed, Y. / Dirr, H.W. / Achilonu, I.
History
DepositionJun 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 24, 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_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-mu 26 kDa isozyme
B: Glutathione S-transferase class-mu 26 kDa isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1039
Polymers51,0692
Non-polymers1,0347
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-63 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.440, 89.260, 91.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutathione S-transferase class-mu 26 kDa isozyme / GST 26 / Sj26 antigen / SjGST


Mass: 25534.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata) / Production host: Escherichia coli DH1 (bacteria) / References: UniProt: P08515, glutathione transferase

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Non-polymers , 5 types, 350 molecules

#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#5: Chemical ChemComp-REF / 2,3,7,8-tetrahydroxychromeno[5,4,3-cde]chromene-5,10-dione / Ellagic acid, 4,4',5,5',6,6'-Hexahydroxydiphenic acid 2,6,2',6'-dilactone


Mass: 302.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H6O8 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 8.5 mg/ml SjGST in 10 mM Tris HCl, pH 7.0 was crystallised in 0.2M sodium chloride, 0.1 M BIS-TRIS, pH 5.5, 25% (w/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.53→45.86 Å / Num. obs: 70333 / % possible obs: 99.6 % / Redundancy: 12.8 % / Biso Wilson estimate: 22.505 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.03 / Rrim(I) all: 0.108 / Net I/σ(I): 12.9
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3463 / CC1/2: 0.322 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ua5

1ua5


Resolution: 1.53→45.86 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 22.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2158 3518 5.01 %
Rwork0.1856 --
obs0.1871 70263 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.53→45.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3554 0 66 345 3965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143805
X-RAY DIFFRACTIONf_angle_d1.315158
X-RAY DIFFRACTIONf_dihedral_angle_d4.4153174
X-RAY DIFFRACTIONf_chiral_restr0.066534
X-RAY DIFFRACTIONf_plane_restr0.008658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.5510.32531510.31242605X-RAY DIFFRACTION99
1.551-1.57310.32791650.31632590X-RAY DIFFRACTION98
1.5731-1.59660.35031490.3052609X-RAY DIFFRACTION100
1.5966-1.62160.28651500.28172613X-RAY DIFFRACTION98
1.6216-1.64820.28431420.27422618X-RAY DIFFRACTION100
1.6482-1.67660.36291370.30122623X-RAY DIFFRACTION99
1.6766-1.70710.35671560.29852648X-RAY DIFFRACTION99
1.7071-1.73990.32221220.29062629X-RAY DIFFRACTION100
1.7399-1.77540.32351140.27282648X-RAY DIFFRACTION99
1.7754-1.8140.30881490.23212647X-RAY DIFFRACTION100
1.814-1.85620.24441340.20752661X-RAY DIFFRACTION99
1.8562-1.90270.2451270.20212640X-RAY DIFFRACTION99
1.9027-1.95410.24951500.19662650X-RAY DIFFRACTION100
1.9541-2.01160.20041320.19022666X-RAY DIFFRACTION100
2.0116-2.07650.24821210.19692701X-RAY DIFFRACTION100
2.0765-2.15070.22261420.18632662X-RAY DIFFRACTION100
2.1507-2.23690.19561330.18112687X-RAY DIFFRACTION100
2.2369-2.33870.23271450.1762678X-RAY DIFFRACTION100
2.3387-2.46190.22031400.17872685X-RAY DIFFRACTION100
2.4619-2.61620.20331390.18242685X-RAY DIFFRACTION100
2.6162-2.81810.20481250.18812723X-RAY DIFFRACTION100
2.8181-3.10170.22181570.18092695X-RAY DIFFRACTION100
3.1017-3.55040.18111650.17642716X-RAY DIFFRACTION100
3.5504-4.47250.16861420.14372752X-RAY DIFFRACTION100
4.4725-45.88060.20321310.16872914X-RAY DIFFRACTION100

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