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- PDB-2hnl: Structure of the prostaglandin D synthase from the parasitic nema... -

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Basic information

Entry
Database: PDB / ID: 2hnl
TitleStructure of the prostaglandin D synthase from the parasitic nematode Onchocerca volvulus
ComponentsGlutathione S-transferase 1
KeywordsTRANSFERASE / Prostaglandin synthase / Glutathione S-transferase / River blindness / Onchocerca volvulus / Immune modulation
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity
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 / 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 / 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
GLUTATHIONE / Glutathione S-transferase 1
Similarity search - Component
Biological speciesOnchocerca volvulus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPerbandt, M. / Hoppner, J. / Betzel, C. / Liebau, E.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure of the extracellular glutathione S-transferase OvGST1 from the human pathogenic parasite Onchocerca volvulus.
Authors: Perbandt, M. / Hoppner, J. / Burmeister, C. / Luersen, K. / Betzel, C. / Liebau, E.
History
DepositionJul 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2011Group: Non-polymer description
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Aug 30, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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: Glutathione S-transferase 1
B: Glutathione S-transferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0544
Polymers51,4392
Non-polymers6152
Water7,476415
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.783, 90.995, 106.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutathione S-transferase 1


Mass: 25719.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Onchocerca volvulus (invertebrata) / Gene: GST1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: P46434, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Reservoir: 22% PEG4000, 10% Isopropanol, 0.1M Hepes pH 7.5 Protein stock: 5.5mg/ml in 100mM Na-acetate-trihydrate pH 8.0, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.803 Å
DetectorDate: Dec 22, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.803 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 34249 / % possible obs: 99.7 % / Rmerge(I) obs: 0.069 / Χ2: 1.025 / Net I/σ(I): 15.1
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.030.3617001.039199
2.03-2.070.32316721.042199.3
2.07-2.110.28716771.097199.8
2.11-2.150.2616521.055199.5
2.15-2.20.24817101.084199.7
2.2-2.250.22716681.08199.6
2.25-2.310.2117100.983199.8
2.31-2.370.16816720.966199.8
2.37-2.440.13617050.989199.8
2.44-2.520.12216831.031100
2.52-2.610.11317121.0041100
2.61-2.710.10116931.004199.9
2.71-2.840.08917091.002199.9
2.84-2.990.0717170.9921100
2.99-3.170.05717280.9931100
3.17-3.420.04417191.0111100
3.42-3.760.04217191.0831100
3.76-4.310.03617561.0141100
4.31-5.430.03317751.0441100
5.43-500.03118721.001199

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Phasing

Phasing MRRfactor: 0.606 / Cor.coef. Fo:Fc: 0.071
Highest resolutionLowest resolution
Rotation3.5 Å45.8 Å
Translation3.5 Å45.8 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1PD2

1pd2


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.542 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1711 5.1 %RANDOM
Rwork0.181 ---
all0.184 ---
obs0.184 33856 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.275 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2--0.92 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3267 0 40 415 3722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223379
X-RAY DIFFRACTIONr_bond_other_d0.0020.023100
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.9714559
X-RAY DIFFRACTIONr_angle_other_deg1.08137226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6285400
X-RAY DIFFRACTIONr_chiral_restr0.2210.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023670
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02686
X-RAY DIFFRACTIONr_nbd_refined0.2180.2750
X-RAY DIFFRACTIONr_nbd_other0.2480.23710
X-RAY DIFFRACTIONr_nbtor_other0.0890.21946
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2289
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.217
X-RAY DIFFRACTIONr_mcbond_it0.9911.51996
X-RAY DIFFRACTIONr_mcangle_it1.83623229
X-RAY DIFFRACTIONr_scbond_it2.80231383
X-RAY DIFFRACTIONr_scangle_it4.5374.51330
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.262 101
Rwork0.174 2331
obs-2432

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