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- PDB-4l5l: Crystal structure of 26 kDa GST of Clonorchis sinensis in P212121... -

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Basic information

Entry
Database: PDB / ID: 4l5l
TitleCrystal structure of 26 kDa GST of Clonorchis sinensis in P212121 symmetry
ComponentsPutative glutathione transferase
KeywordsTRANSFERASE / GSH Binding
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process / metal ion binding
Similarity search - Function
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 / 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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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 / glutathione transferase
Similarity search - Component
Biological speciesClonorchis sinensis (oriental liver fluke)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsChung, Y.J. / Han, Y.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Crystal structures of 26kDa Clonorchis sinensis glutathione S-transferase reveal zinc binding and putative metal binding.
Authors: Han, Y.H. / Hong, S.J. / Cheong, H.K. / Chung, Y.J.
History
DepositionJun 11, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Putative glutathione transferase
B: Putative glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2678
Polymers50,1312
Non-polymers1,1366
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-67 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.272, 67.455, 120.701
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 Putative glutathione transferase


Mass: 25065.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clonorchis sinensis (oriental liver fluke)
Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q25595
#2: Chemical ChemComp-GSH / GLUTATHIONE


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH6.5, 5mM Zinc sulfate, 10% PEG MME 550, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.23985 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionResolution: 2.2→60.3 Å / Num. obs: 27909 / % possible obs: 99 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 19.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.284.40.172198.5
2.28-2.374.70.143198.7
2.37-2.484.90.12198.9
2.48-2.615.10.102199.1
2.61-2.775.30.085199.4
2.77-2.995.50.07199.3
2.99-3.295.80.06199.6
3.29-3.766.10.049199.7
3.76-4.746.10.04199.6
4.74-505.80.037197.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.55 Å37.22 Å
Translation2.55 Å37.22 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→37.24 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.002 / SU ML: 0.13 / SU R Cruickshank DPI: 0.2491 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 1404 5 %RANDOM
Rwork0.17732 ---
obs0.18035 26486 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.295 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2---1.34 Å2-0 Å2
3---2.04 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3516 0 66 179 3761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193691
X-RAY DIFFRACTIONr_bond_other_d0.0010.023434
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.9755009
X-RAY DIFFRACTIONr_angle_other_deg0.87237908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0765434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05423.82178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.20615594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2961521
X-RAY DIFFRACTIONr_chiral_restr0.1040.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214177
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02896
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0181.52184
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.80223516
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.89831541
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2674.51537
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 102 -
Rwork0.176 1897 -
obs--97.61 %

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