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- PDB-7unn: Thiol-disulfide oxidoreductase TsdA from Corynebacterium diphtheriae -

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Basic information

Entry
Database: PDB / ID: 7unn
TitleThiol-disulfide oxidoreductase TsdA from Corynebacterium diphtheriae
ComponentsThioredoxin domain-containing protein
KeywordsOXIDOREDUCTASE / TsdA / thiol disulfide / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyThioredoxin / Thioredoxin-like fold / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / Thioredoxin domain-containing protein
Function and homology information
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsOsipiuk, J. / Reardon-Robinson, M. / Nguyen, M.T. / Sanchez, B. / Ton-That, H. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)5R01DE025015-08 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: A cryptic oxidoreductase safeguards oxidative protein folding in Corynebacterium diphtheriae.
Authors: Reardon-Robinson, M.E. / Nguyen, M.T. / Sanchez, B.C. / Osipiuk, J. / Ruckert, C. / Chang, C. / Chen, B. / Nagvekar, R. / Joachimiak, A. / Tauch, A. / Das, A. / Ton-That, H.
History
DepositionApr 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2136
Polymers27,9301
Non-polymers2845
Water5,260292
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.174, 65.356, 68.852
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 Thioredoxin domain-containing protein


Mass: 27929.521 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: CIP107518_01391 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A6J4WJ52
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.11 Å3/Da / Density % sol: 41.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 6.4 % PEG 200, 21.4 % PEG 2000, 50 mM acetate buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.45→30.48 Å / Num. obs: 42523 / % possible obs: 99.4 % / Redundancy: 6.3 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.035 / Rrim(I) all: 0.091 / Χ2: 1.586 / Net I/av σ(I): 25.3 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.45-1.482.80.9511.0918510.450.7880.6291.1511.10589.6
1.48-1.53.40.7821020.5470.4830.9261.12699
1.5-1.533.90.721290.6990.40.8121.21100
1.53-1.564.80.6420870.7770.3240.721.244100
1.56-1.65.60.54420990.8590.2530.6011.279100
1.6-1.6360.47121310.8930.210.5161.336100
1.63-1.676.60.39721070.930.1680.4311.346100
1.67-1.727.20.37121140.9440.1480.3991.373100
1.72-1.777.20.29321220.9660.1180.3161.448100
1.77-1.837.20.24821170.9750.0990.2671.498100
1.83-1.897.20.19221120.9840.0770.2071.62100
1.89-1.977.20.15521220.9880.0620.1671.694100
1.97-2.067.20.12621400.9890.050.1361.766100
2.06-2.177.20.10921420.9920.0430.1171.772100
2.17-2.37.30.09621270.9930.0380.1031.775100
2.3-2.487.20.08521730.9950.0340.0911.793100
2.48-2.737.20.0821580.9950.0320.0861.871100
2.73-3.127.20.06921750.9960.0270.0741.864100
3.12-3.947.10.05422030.9980.0210.0581.747100
3.94-30.486.50.05223120.9970.0220.0561.69799.3

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→30.48 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.976 / SU B: 2.39 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1526 2097 4.9 %RANDOM
Rwork0.1138 ---
obs0.1158 40362 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.39 Å2 / Biso mean: 19.163 Å2 / Biso min: 10.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.07 Å2-0 Å2
3----0.4 Å2
Refinement stepCycle: final / Resolution: 1.45→30.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 17 292 2166
Biso mean--31.92 34.98 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132062
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151950
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.6612818
X-RAY DIFFRACTIONr_angle_other_deg1.5071.5874556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06423.519108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54915349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4851511
X-RAY DIFFRACTIONr_chiral_restr0.0850.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022408
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02458
X-RAY DIFFRACTIONr_rigid_bond_restr2.19334012
LS refinement shellResolution: 1.45→1.483 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.286 138 -
Rwork0.268 2678 -
obs--90.4 %

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