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- PDB-7uno: Thiol-disulfide oxidoreductase TsdA, C129S mutant, from Corynebac... -

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Basic information

Entry
Database: PDB / ID: 7uno
TitleThiol-disulfide oxidoreductase TsdA, C129S mutant, 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 / TRIETHYLENE GLYCOL / Thioredoxin domain-containing protein
Function and homology information
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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: To Be Published
Title: Thiol-disulfide oxidoreductase in Corynebacterium diphtheriae
Authors: Osipiuk, J. / Reardon-Robinson, M. / Nguyen, M.T. / Sanchez, B. / Ton-That, H. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: Thioredoxin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0674
Polymers27,8201
Non-polymers2483
Water7,476415
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.809, 65.114, 69.422
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: 27819.666 Da / Num. of mol.: 1 / Mutation: C129S
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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.15 Å3/Da / Density % sol: 42.66 %
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-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.1→47.49 Å / Num. obs: 95848 / % possible obs: 98.2 % / Redundancy: 7.6 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.02 / Rrim(I) all: 0.068 / Χ2: 1.588 / Net I/av σ(I): 40.1 / Net I/σ(I): 12.3
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
1.1-1.122.20.7991.2539080.4580.7930.6111.0130.96680.6
1.12-1.142.80.71142240.5360.4880.8691.06788.7
1.14-1.163.50.64346050.6660.390.7571.15594.9
1.16-1.184.40.58647490.7730.3110.6661.20298.7
1.18-1.215.70.55248300.880.2490.6071.234100
1.21-1.246.70.46848390.9250.1930.5061.296100
1.24-1.276.90.41248360.9420.1680.4451.319100
1.27-1.36.90.33248530.960.1350.3591.382100
1.3-1.346.90.28748340.9690.1160.311.448100
1.34-1.3970.2448510.9790.0970.2591.506100
1.39-1.4470.20148430.9840.0810.2171.535100
1.44-1.4970.15748570.990.0630.171.664100
1.49-1.5670.12548890.9920.050.1351.702100
1.56-1.647.10.10248620.9940.0410.111.703100
1.64-1.757.10.08648940.9950.0340.0921.63100
1.75-1.887.10.07549040.9960.030.0811.671100
1.88-2.0713.20.09949060.9970.0280.1031.73100
2.07-2.3714.20.08349470.9980.0230.0861.817100
2.37-2.9913.80.05649960.9990.0160.0581.781100
2.991-47.4912.40.03952210.9990.0120.0411.70599.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7UNN

7unn


Resolution: 1.1→47.49 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.7 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1339 4730 4.9 %RANDOM
Rwork0.1162 ---
obs0.1171 91039 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.54 Å2 / Biso mean: 14.865 Å2 / Biso min: 7.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å20 Å2
2--0.2 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.1→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1861 0 15 416 2292
Biso mean--28.18 30.6 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132162
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152040
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.6592975
X-RAY DIFFRACTIONr_angle_other_deg1.541.5874789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1125316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.95922.627118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.06115379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1381515
X-RAY DIFFRACTIONr_chiral_restr0.0880.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022559
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02495
X-RAY DIFFRACTIONr_rigid_bond_restr1.42434202
LS refinement shellResolution: 1.1→1.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 304 -
Rwork0.317 5559 -
all-5863 -
obs--82.43 %

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