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- PDB-2voc: THIOREDOXIN A ACTIVE SITE MUTANTS FORM MIXED DISULFIDE DIMERS THA... -

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Basic information

Entry
Database: PDB / ID: 2voc
TitleTHIOREDOXIN A ACTIVE SITE MUTANTS FORM MIXED DISULFIDE DIMERS THAT RESEMBLE ENZYME-SUBSTRATE REACTION INTERMEDIATE
ComponentsTHIOREDOXIN
KeywordsELECTRON TRANSPORT / THIOREDOXIN / THIOREDOXIN FOLD / BACILLUS / HOMODIMER / DISULFIDE / TRANSPORT / REDOX-ACTIVE CENTER
Function / homology
Function and homology information


protein-disulfide reductase activity / cell redox homeostasis / cytosol / cytoplasm
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
DI(HYDROXYETHYL)ETHER / Thioredoxin
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKouwen, T.R.H.M. / Andrell, J. / Schrijver, R. / Dubois, J.Y.F. / Maher, M.J. / Iwata, S. / Carpenter, E.P. / van Dijl, J.M.
CitationJournal: J. Mol. Biol. / Year: 2008
Title: Thioredoxin A active-site mutants form mixed disulfide dimers that resemble enzyme-substrate reaction intermediates.
Authors: Kouwen, T.R. / Andrell, J. / Schrijver, R. / Dubois, J.Y. / Maher, M.J. / Iwata, S. / Carpenter, E.P. / van Dijl, J.M.
History
DepositionFeb 13, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Feb 28, 2018Group: Atomic model / Database references / Source and taxonomy
Category: atom_site / citation ...atom_site / citation / citation_author / entity_src_gen
Item: _atom_site.occupancy / _citation.journal_abbrev ..._atom_site.occupancy / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.1Dec 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
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THIOREDOXIN
B: THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0253
Polymers24,9182
Non-polymers1061
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-4.4 kcal/mol
Surface area13890 Å2
MethodPQS
Unit cell
Length a, b, c (Å)36.765, 38.395, 41.878
Angle α, β, γ (deg.)83.33, 66.62, 78.08
Int Tables number1
Space group name H-MP1

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Components

#1: Protein THIOREDOXIN / TRX / THIOREDOXIN A


Mass: 12459.224 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: HOMODIMER THROUGH RESIDUE C29 DISULFIDE BOND
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Plasmid: PET-26B / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: P14949
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 32 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 32 TO SER
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: 2.13 Å3/Da / Density % sol: 42.35 % / Description: NONE
Crystal growpH: 7.8
Details: 0.1 M TRIS PH 7.8, 0.1 M MAGNESIUM CHLORIDE, 4% ACETONITRILE, 35% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 10, 2006 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 31147 / % possible obs: 94.5 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.9 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: POLYSERINE MODEL OF PDB ENTRY 2TRX

2trx


Resolution: 1.5→22.95 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.954 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: SIDE-CHAIN ATOMS FOR WHICH THERE WERE NO ELECTRON DENSITY WERE DELETED FROM THE COORDINATE FILE.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1570 5 %RANDOM
Rwork0.185 ---
obs0.188 29577 100 %-
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: 18.18 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20.06 Å2-0.59 Å2
2---0.46 Å2-0.97 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.5→22.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 7 254 1890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221740
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0481.9672374
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8195228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28927.18371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09815306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1350.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021294
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2590.2808
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21200
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2216
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3271.51130
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.96321793
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0883687
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6674.5578
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.325 109
Rwork0.276 2026
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8682-0.1462-0.10611.38440.51351.17080.020.09540.0432-0.1384-0.0111-0.0261-0.098-0.0007-0.0090.0809-0.0041-0.00640.09070.01840.080426.86272.945933.9136
20.93790.27380.1961.25240.14631.03730.0011-0.0155-0.09230.02110.0018-0.11330.07050.0989-0.0030.08360.00650.00110.07920.0050.071738.545426.34151.9314
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 111
2X-RAY DIFFRACTION2B2 - 105

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