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- PDB-5nii: Crystal structure of the atypical thioredoxin reductase TRi from ... -

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Basic information

Entry
Database: PDB / ID: 5nii
TitleCrystal structure of the atypical thioredoxin reductase TRi from Desulfovibrio vulgaris Hildenborough
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / Thioredoxin reductase / Desulfovibrio / Anaerobes / Disulfide stress / NADPH motif
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
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
FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin reductase, putative
Similarity search - Component
Biological speciesDesulfovibrio vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsValette, O. / Tran, T.T.I. / Cavazza, C. / Caudeville, E. / Brasseur, G. / Dolla, A. / Talla, E. / Pieulle, L.
CitationJournal: Front Microbiol / Year: 2017
Title: Biochemical Function, Molecular Structure and Evolution of an Atypical Thioredoxin Reductase from Desulfovibrio vulgaris.
Authors: Valette, O. / Tran, T.T.T. / Cavazza, C. / Caudeville, E. / Brasseur, G. / Dolla, A. / Talla, E. / Pieulle, L.
History
DepositionMar 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,66015
Polymers65,3712
Non-polymers2,28813
Water5,729318
1
A: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,06111
Polymers32,6861
Non-polymers1,37510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5994
Polymers32,6861
Non-polymers9133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.387, 148.161, 152.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-408-

CL

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thioredoxin reductase /


Mass: 32685.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria)
Gene: DVU_1457 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72C27

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Non-polymers , 5 types, 331 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 12% PEG 3350, 100 mM BisTris pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→47.48 Å / Num. obs: 92563 / % possible obs: 99.2 % / Redundancy: 3.67 % / Net I/σ(I): 16.24

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FD8

3fd8


Resolution: 2→47.48 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.41
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 2540 5 %RANDOM
Rwork0.1944 ---
obs0.1961 50800 98.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4402 0 147 318 4867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114648
X-RAY DIFFRACTIONf_angle_d1.2896301
X-RAY DIFFRACTIONf_dihedral_angle_d14.9271747
X-RAY DIFFRACTIONf_chiral_restr0.055701
X-RAY DIFFRACTIONf_plane_restr0.005821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9999-2.03840.33581340.32322530X-RAY DIFFRACTION95
2.0384-2.080.34661410.31062690X-RAY DIFFRACTION100
2.08-2.12520.3531390.28082632X-RAY DIFFRACTION99
2.1252-2.17470.33911410.27282674X-RAY DIFFRACTION99
2.1747-2.22910.32561390.25932636X-RAY DIFFRACTION99
2.2291-2.28930.2731410.23892676X-RAY DIFFRACTION99
2.2893-2.35670.26541410.23072681X-RAY DIFFRACTION100
2.3567-2.43280.30161420.22372695X-RAY DIFFRACTION100
2.4328-2.51970.27661390.21442652X-RAY DIFFRACTION100
2.5197-2.62060.25841410.21872677X-RAY DIFFRACTION100
2.6206-2.73980.26251410.21072680X-RAY DIFFRACTION99
2.7398-2.88430.26031420.20932698X-RAY DIFFRACTION100
2.8843-3.06490.22571420.20752686X-RAY DIFFRACTION100
3.0649-3.30150.22371420.19982706X-RAY DIFFRACTION99
3.3015-3.63370.22481400.18322660X-RAY DIFFRACTION98
3.6337-4.15920.19941440.15962739X-RAY DIFFRACTION99
4.1592-5.23910.19691430.15252716X-RAY DIFFRACTION98
5.2391-47.49350.17281480.17592832X-RAY DIFFRACTION98

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