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- PDB-4ruv: Crystal structure of thioredoxin 2 from Staphylococcus aureus NCTC8325 -

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Basic information

Entry
Database: PDB / ID: 4ruv
TitleCrystal structure of thioredoxin 2 from Staphylococcus aureus NCTC8325
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / electron transport
Function / homology
Function and homology information


protein-disulfide reductase activity / cell redox homeostasis / cytosol / cytoplasm
Similarity search - Function
: / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin, putative
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å
AuthorsBose, M. / Biswas, R. / Roychowdhury, A. / Bhattacharyya, S. / Ghosh, A.K. / Das, A.K.
CitationJournal: Biochimie / Year: 2019
Title: Elucidation of the mechanism of disulfide exchange between staphylococcal thioredoxin2 and thioredoxin reductase2: A structural insight.
Authors: Bose, M. / Bhattacharyya, S. / Biswas, R. / Roychowdhury, A. / Bhattacharjee, A. / Ghosh, A.K. / Das, A.K.
History
DepositionNov 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)13,1251
Polymers13,1251
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.376, 31.376, 94.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Thioredoxin


Mass: 13124.634 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Strain: NCTC8325 / Gene: SAOUHSC_00834 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q2G000
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.78 Å3/Da / Density % sol: 30.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Na-HEPES pH 7.5, 1.4 M sodium citrate tribasic dihydrate , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 15, 2014 / Details: varimax
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.926→18.92 Å / Num. all: 6850 / Num. obs: 6850 / % possible obs: 98.2 % / Redundancy: 3.5 % / Rsym value: 0.115 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.93-2.032.80.2862.50.286189.1
2.03-2.153.50.2412.80.241199.8
2.15-2.33.60.2093.10.209199.9
2.3-2.493.60.1823.70.182199.9
2.49-2.723.60.14940.1491100
2.72-3.053.60.1454.20.1451100
3.05-3.523.70.0996.20.0991100
3.52-4.313.70.09360.0931100
4.31-6.093.70.0696.80.0691100
6.09-18.9613.50.05210.10.052196.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.27 Å18.91 Å
Translation4.27 Å18.91 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASER2.5.0phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FA4

2fa4


Resolution: 1.93→18.92 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.138 / SU ML: 0.122 / SU R Cruickshank DPI: 0.1806 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23936 323 4.7 %RANDOM
Rwork0.16971 ---
obs0.17297 6500 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.157 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å2-0 Å2
2---0.26 Å2-0 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.93→18.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms829 0 0 62 891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.019855
X-RAY DIFFRACTIONr_bond_other_d0.0010.02783
X-RAY DIFFRACTIONr_angle_refined_deg1.9371.9371166
X-RAY DIFFRACTIONr_angle_other_deg1.01331809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9275107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30626.15439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.85915140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.168151
X-RAY DIFFRACTIONr_chiral_restr0.1620.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021971
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02186
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.926→1.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 20 -
Rwork0.231 370 -
obs--77.08 %

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