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- PDB-2vim: X-ray structure of Fasciola hepatica thioredoxin -

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Basic information

Entry
Database: PDB / ID: 2vim
TitleX-ray structure of Fasciola hepatica thioredoxin
ComponentsTHIOREDOXIN
KeywordsOXIDOREDUCTASE / THIOREDOXIN / TRX / THIOREDOXIN FOLD
Function / homology
Function and homology information


protein-disulfide reductase activity
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesFASCIOLA HEPATICA (liver fluke)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsLine, K. / Isupov, M.N. / Garcia-Rodriguez, E. / Maggioli, G. / Parra, F. / Littlechild, J.A.
Citation
Journal: Mol.Biochem.Parasitol. / Year: 2008
Title: The Fasciola Hepatica Thioredoxin: High Resolution Structure Reveals Two Oxidation States.
Authors: Line, K. / Isupov, M.N. / Garcia-Rodriguez, E. / Maggioli, G. / Parra, F. / Littlechild, J.A.
#1: Journal: Parasitol.Res. / Year: 2001
Title: Heterologous Expression and Functional Characterisation of Thioredoxin from Fasciola Hepatica.
Authors: Salazar-Calderon, M. / Martin-Alonso, J.M. / Ruiz De Eguino, A.D. / Parra, F.
History
DepositionDec 5, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)11,7001
Polymers11,7001
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)32.666, 34.586, 40.381
Angle α, β, γ (deg.)90.00, 106.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein THIOREDOXIN / TRX


Mass: 11700.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) FASCIOLA HEPATICA (liver fluke) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q9U1G7, phosphoadenylyl-sulfate reductase (thioredoxin)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.87 Å3/Da / Density % sol: 33.86 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.1 M TRIS-HCL PH 8.5, 2 M AMMONIUM SULFATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 10, 2004 / Details: MIRRORS
RadiationMonochromator: SI(111) DOUBLE CRYSTAL, NON DISPERSIVE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.38→38.69 Å / Num. obs: 16069 / % possible obs: 89.6 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.75
Reflection shellResolution: 1.38→1.42 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 0.87 / % possible all: 56.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
Babelphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FA4

2fa4


Resolution: 1.38→38.69 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.276 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ACTIVE SITE CYSTEINE RESIDUES MODELLED IN BOTH REDUCED AND DISULFIDE OXIDATION STATES
RfactorNum. reflection% reflectionSelection details
Rfree0.248 807 5 %RANDOM
Rwork0.189 ---
obs0.192 15244 89.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å21.71 Å2
2---1.21 Å20 Å2
3---2.98 Å2
Refinement stepCycle: LAST / Resolution: 1.38→38.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms821 0 0 103 924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022887
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.9681211
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9435123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.9292542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6215171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.876156
X-RAY DIFFRACTIONr_chiral_restr0.1240.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02676
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.2449
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.2617
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2920.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6274570
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.6966900
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.868354
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.35710301
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: 1.38→1.42 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.409 39
Rwork0.362 695

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