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- PDB-5vt3: High resolution structure of thioredoxin-disulfide reductase from... -

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Basic information

Entry
Database: PDB / ID: 5vt3
TitleHigh resolution structure of thioredoxin-disulfide reductase from Vibrio vulnificus CMCP6 in complex with NADP and FAD
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 / 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 superfamily
Similarity search - Domain/homology
CACODYLATE ION / FLAVIN-ADENINE DINUCLEOTIDE / : / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Thioredoxin reductase
Similarity search - Component
Biological speciesVibrio vulnificus CMCP6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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
DepositionMay 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.3Mar 5, 2025Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Mar 25, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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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)72,90412
Polymers69,3102
Non-polymers3,59410
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-27 kcal/mol
Surface area24260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.931, 100.758, 126.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thioredoxin reductase


Mass: 34654.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus CMCP6 (bacteria) / Gene: trxB, VFL11327_00718
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1L9L8C0, thioredoxin-disulfide reductase (NADPH)

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Non-polymers , 6 types, 467 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 12 mM POTASSIUM CHLORIDE, 80 mM Potassium Chloride, 40 MM SODIUM CACODYLATE, 40% MPD, 12 MM SPERMIDINE TETRAHYDROCHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.98→40.565 Å / Num. obs: 55371 / % possible obs: 98.7 % / Redundancy: 6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.55
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 2 / Num. unique obs: 2444 / % possible all: 87.3

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Processing

Software
NameVersionClassification
PHENIXdev_2650refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5USX

5usx


Resolution: 1.98→40.565 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.02
RfactorNum. reflection% reflection
Rfree0.1975 2561 5.15 %
Rwork0.1518 --
obs0.1541 49759 88.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 157.99 Å2 / Biso mean: 30.4273 Å2 / Biso min: 8.41 Å2
Refinement stepCycle: final / Resolution: 1.98→40.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4751 0 226 457 5434
Biso mean--30.16 40.11 -
Num. residues----632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135283
X-RAY DIFFRACTIONf_angle_d1.3637214
X-RAY DIFFRACTIONf_chiral_restr0.083798
X-RAY DIFFRACTIONf_plane_restr0.007934
X-RAY DIFFRACTIONf_dihedral_angle_d18.7063112
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9795-2.01760.2894630.2111196125941
2.0176-2.05880.2914810.19381571165254
2.0588-2.10360.23421120.19131927203966
2.1036-2.15250.2421110.18642172228374
2.1525-2.20630.24451300.18062360249081
2.2063-2.2660.20781460.16772545269187
2.266-2.33260.25921530.16812706285993
2.3326-2.40790.22121490.16642883303298
2.4079-2.4940.22291400.164329373077100
2.494-2.59380.21531690.158629383107100
2.5938-2.71180.20541650.153729463111100
2.7118-2.85480.23311510.155329413092100
2.8548-3.03360.20141400.157929653105100
3.0336-3.26770.20981720.14929693141100
3.2677-3.59640.17071620.138929643126100
3.5964-4.11630.1611610.121130083169100
4.1163-5.18440.1581840.126730023186100
5.1844-40.5740.19191720.166931683340100
Refinement TLS params.Method: refined / Origin x: 37.834 Å / Origin y: 86.6515 Å / Origin z: 26.3927 Å
111213212223313233
T0.0868 Å20.0024 Å20.0114 Å2-0.0871 Å2-0.0177 Å2--0.0884 Å2
L0.6088 °2-0.3268 °20.5521 °2-0.7923 °2-0.6933 °2--0.7969 °2
S0.0396 Å °0.0044 Å °-0.0026 Å °-0.0402 Å °0.0379 Å °0.0179 Å °0.0565 Å °-0.0336 Å °0.1169 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 576
2X-RAY DIFFRACTION1allA403 - 405
3X-RAY DIFFRACTION1allB-1 - 317
4X-RAY DIFFRACTION1allB401 - 539
5X-RAY DIFFRACTION1allB403 - 405
6X-RAY DIFFRACTION1allD1 - 378

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