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- PDB-5utx: Crystal structure of thioredoxin-disulfide reductase from Vibrio ... -

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Basic information

Entry
Database: PDB / ID: 5utx
TitleCrystal structure of thioredoxin-disulfide reductase from Vibrio vulnificus CMCP6 - apo form
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center For Structural Genomics Of Infectious Diseases / CSGID / thioredoxin-disulfide reductase
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / nucleotide binding / cytoplasm
Similarity search - Function
Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / : / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Thioredoxin reductase
Similarity search - Component
Biological speciesVibrio vulnificus CMCP6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsChang, C. / Grimshaw, S. / Maltseva, N. / Mulligan, R. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2025
Title: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.
Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionFeb 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.4Jun 18, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin reductase
B: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9554
Polymers68,7652
Non-polymers1902
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-30 kcal/mol
Surface area25840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.031, 120.031, 79.185
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Thioredoxin reductase / thioredoxin-disulfide reductase


Mass: 34382.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus CMCP6 (bacteria) / Gene: VV1455
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q7MLH2, thioredoxin-disulfide reductase (NADPH)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE PROTEIN SEQUENCE MATCHES TO GENBANK 27366093.

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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: 2.39 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 20% PEG1000, 100 mM potassium/sodium phosphate, 200 mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 24257 / % possible obs: 98.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 34.06 Å2 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Χ2: 0.933 / Net I/σ(I): 9.7 / Num. measured all: 160021
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.495.80.960.6980.4191.0520.92475.7
2.49-2.546.60.8290.7440.3410.8990.942100
2.54-2.596.80.690.8380.2810.7470.946100
2.59-2.646.80.5490.8780.2230.5940.95100
2.64-2.76.80.4580.9090.1860.4960.96899.9
2.7-2.766.70.3790.9380.1550.410.971100
2.76-2.836.60.310.9570.1280.3371100
2.83-2.960.2570.9580.1120.2821.00899.9
2.9-2.996.80.2130.9740.0860.2310.988100
2.99-3.096.90.1780.9850.0710.1921.039100
3.09-3.26.80.1370.9880.0550.1481.021100
3.2-3.326.80.1080.9880.0440.1171.05699.9
3.32-3.486.50.0860.9930.0360.0941.01499.9
3.48-3.666.20.0740.9940.0310.0810.99299.9
3.66-3.896.90.0610.9960.0240.0650.895100
3.89-4.196.80.0540.9960.0220.0590.861100
4.19-4.616.50.0480.9970.020.0520.81899.8
4.61-5.286.70.0490.9970.020.0530.84299.7
5.28-6.656.60.0480.9960.020.0520.772100
6.65-506.10.040.9970.0170.0440.66299.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXdev_2614refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CL0

1cl0


Resolution: 2.46→47.83 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.93
RfactorNum. reflection% reflection
Rfree0.2538 1164 4.95 %
Rwork0.1996 --
obs0.2023 23504 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.73 Å2 / Biso mean: 50.8994 Å2 / Biso min: 5.41 Å2
Refinement stepCycle: final / Resolution: 2.46→47.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4286 0 10 109 4405
Biso mean--43.12 38.72 -
Num. residues----580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024379
X-RAY DIFFRACTIONf_angle_d0.4785928
X-RAY DIFFRACTIONf_chiral_restr0.041681
X-RAY DIFFRACTIONf_plane_restr0.004779
X-RAY DIFFRACTIONf_dihedral_angle_d9.6952598
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4602-2.57210.3255860.25212233231977
2.5721-2.70770.30651750.23612782295799
2.7077-2.87740.30891710.230828333004100
2.8774-3.09950.29661190.226928742993100
3.0995-3.41130.2591410.214328833024100
3.4113-3.90480.24171600.185528613021100
3.9048-4.91880.23041610.165228793040100
4.9188-47.83910.21371510.19032995314699
Refinement TLS params.Method: refined / Origin x: 78.7074 Å / Origin y: 10.735 Å / Origin z: 4.6334 Å
111213212223313233
T0.1477 Å20.071 Å20.1087 Å2-0.0059 Å2-0.0541 Å2--0.1482 Å2
L0.1179 °2-0.0144 °20.0172 °2-0.156 °20.0776 °2--0.1442 °2
S0.0473 Å °0.1208 Å °-0.2732 Å °-0.028 Å °-0.0384 Å °-0.2388 Å °0.1641 Å °-0.047 Å °0.021 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 315
2X-RAY DIFFRACTION1allB4 - 317
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allS1 - 109

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