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- PDB-2wgr: Combining crystallography and molecular dynamics: The case of Sch... -

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Basic information

Entry
Database: PDB / ID: 2wgr
TitleCombining crystallography and molecular dynamics: The case of Schistosoma mansoni phospholipid glutathione peroxidase
ComponentsGLUTATHIONE PEROXIDASE
KeywordsOXIDOREDUCTASE / SELENIUM / SELENOCYSTEINE / SCHISTOSOMIASIS / LIPID GSH PEROXIDASE / MOLECULAR DYNAMICS SIMULATIONS / ROS DETOXIFICATION PATHWAY
Function / homology
Function and homology information


glutathione peroxidase / glutathione peroxidase activity / response to oxidative stress
Similarity search - Function
Glutathione peroxidase active site / Glutathione peroxidases active site. / Glutathione peroxidase / Glutathione peroxidase conserved site / Glutathione peroxidase / Glutathione peroxidases signature 2. / Glutathione peroxidase profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Glutathione peroxidase active site / Glutathione peroxidases active site. / Glutathione peroxidase / Glutathione peroxidase conserved site / Glutathione peroxidase / Glutathione peroxidases signature 2. / Glutathione peroxidase profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYROPHOSPHATE 2- / Glutathione peroxidase
Similarity search - Component
Biological speciesSCHISTOSOMA MANSONI (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDimastrogiovanni, D. / Anselmi, M. / Miele, A.E. / Boumis, G. / Angelucci, F. / Di Nola, A. / Brunori, M. / Bellelli, A.
CitationJournal: Proteins / Year: 2010
Title: Combining Crystallography and Molecular Dynamics: The Case of Schistosoma Mansoni Phospholipid Glutathione Peroxidase.
Authors: Dimastrogiovanni, D. / Anselmi, M. / Miele, A.E. / Boumis, G. / Petersson, L. / Angelucci, F. / Nola, A.D. / Brunori, M. / Bellelli, A.
History
DepositionApr 24, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6132
Polymers19,4371
Non-polymers1761
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.913, 51.170, 90.622
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 GLUTATHIONE PEROXIDASE / PHOSPHOLIPID-HYDROPEROXIDE GLUTATHIONE PEROXIDASE / GPX


Mass: 19437.193 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHISTOSOMA MANSONI (invertebrata) / Plasmid: PGEX-4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q00277, glutathione peroxidase
#2: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SEC 43 TO SER
Sequence detailsU43S MUTATION IN U43S SMGPX

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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: 2.4 Å3/Da / Density % sol: 48.5 % / Description: NONE
Crystal growpH: 6 / Details: 0.2M NAH2PO4, 0.1M MES, 32% PEG-MME 5000, PH 6.0

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Data collection

DiffractionMean temperature: 199 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9185
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9185 Å / Relative weight: 1
ReflectionResolution: 1.7→45.31 Å / Num. obs: 21068 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 9.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4SUITEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V1M

2v1m


Resolution: 1.7→90.54 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 1.737 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21112 1085 5.1 %RANDOM
Rwork0.18203 ---
obs0.18355 19983 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.591 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2---0.38 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.7→90.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1317 0 9 140 1466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221376
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9571859
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8475166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.55124.54566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52915250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.178157
X-RAY DIFFRACTIONr_chiral_restr0.1010.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021034
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.2605
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2934
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.320.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.951.5839
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36821331
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2543607
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2664.5528
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 83 -
Rwork0.204 1474 -
obs--100 %

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