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- PDB-5mjk: Crystal Structure of Lactococcus lactis Thioredoxin Reductase (FO... -

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Basic information

Entry
Database: PDB / ID: 5mjk
TitleCrystal Structure of Lactococcus lactis Thioredoxin Reductase (FO conformation)
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / Thioredoxin Reductase / photosensitivity / Reactive Oxygen Species / FAD si-face open space / Oxygen pocket / FO-FR conformations
Function / homology
Function and homology information


thioredoxin-disulfide reductase / 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
FLAVIN-ADENINE DINUCLEOTIDE / : / Thioredoxin reductase
Similarity search - Component
Biological speciesLactococcus lactis subsp. cremoris (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSkjoldager, N. / Bang, M.B. / Svensson, B. / Hagglund, P. / Harris, P.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Technical University Denmark Denmark
CitationJournal: Sci Rep / Year: 2017
Title: The structure of Lactococcus lactis thioredoxin reductase reveals molecular features of photo-oxidative damage.
Authors: Skjoldager, N. / Blanner Bang, M. / Rykr, M. / Bjornberg, O. / Davies, M.J. / Svensson, B. / Harris, P. / Hagglund, P.
History
DepositionDec 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.4Jan 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)147,63312
Polymers144,1064
Non-polymers3,5268
Water7,152397
1
A: Thioredoxin reductase
B: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8166
Polymers72,0532
Non-polymers1,7634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Thioredoxin reductase
D: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8166
Polymers72,0532
Non-polymers1,7634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.610, 132.260, 73.500
Angle α, β, γ (deg.)90.000, 112.620, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
12
13
14
15
16
/ NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.963441, 0.258835, 0.069172), (0.263199, 0.866137, 0.424892), (0.050065, 0.427564, -0.902598)23.21273, -19.713921, 71.927223
3given(1), (1), (1)
4given(0.432861, -0.256799, -0.86411), (0.290583, -0.867652, 0.403414), (-0.853342, -0.425717, -0.300951)1.90909, -50.31683, 65.009666
5given(1), (1), (1)
6given(-0.385141, 0.003871, 0.92285), (-0.001567, -0.999992, 0.003541), (0.922857, -8.2E-5, 0.385144)12.3645, -35.105598, -8.23152
7given(1), (1), (1)
8given(-0.383279, -0.002266, 0.92363), (-0.001135, -0.999995, -0.002925), (0.923632, -0.00217, 0.383274)12.12393, -34.978161, -8.23277
9given(1), (1), (1)
10given(0.416854, -0.266935, -0.868895), (0.293533, -0.865162, 0.406612), (-0.860274, -0.424547, -0.282292)2.38714, -50.412079, 65.06086
11given(1), (1), (1)
12given(-0.95468, -0.288835, 0.071833), (-0.292612, 0.866685, -0.404025), (0.05444, -0.406734, -0.911923)71.445663, 15.29699, 19.14361

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Components

#1: Protein
Thioredoxin reductase /


Mass: 36026.605 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria)
Gene: N41_1746, NCDO763_0431 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: A0A166TWQ7, UniProt: A2RLJ5*PLUS, thioredoxin-disulfide reductase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 20% PEG4000, 400 mM Li2SO4. DTT added (20 mM DTT final in drop)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→47.36 Å / Num. obs: 86685 / % possible obs: 99 % / Redundancy: 3.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Net I/σ(I): 12.18
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.826 / Mean I/σ(I) obs: 1.82 / CC1/2: 0.633 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GCM

4gcm


Resolution: 2→47.36 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.894 / SU B: 11.468 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.196
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.276 4335 5 %RANDOM
Rwork0.2299 ---
obs0.2322 82350 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 90.86 Å2 / Biso mean: 34.646 Å2 / Biso min: 5.49 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å2-1.05 Å2
2--2.38 Å20 Å2
3----0.67 Å2
Refinement stepCycle: final / Resolution: 2→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9356 0 232 409 9997
Biso mean--25.05 33.83 -
Num. residues----1208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0199772
X-RAY DIFFRACTIONr_bond_other_d0.0030.029168
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.98713232
X-RAY DIFFRACTIONr_angle_other_deg1.0693.00121124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4451204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88224.911448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.293151668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5241552
X-RAY DIFFRACTIONr_chiral_restr0.0920.21440
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211024
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022136
Refine LS restraints NCS
Ens-IDDom-IDNumberRefine-IDTypeRms dev position (Å)Weight position
112736X-RAY DIFFRACTIONTIGHT THERMAL3.760.87
212736X-RAY DIFFRACTIONTIGHT THERMAL3.570.87
312736X-RAY DIFFRACTIONTIGHT THERMAL2.530.87
412736X-RAY DIFFRACTIONTIGHT THERMAL2.040.87
512736X-RAY DIFFRACTIONTIGHT THERMAL3.750.87
612736X-RAY DIFFRACTIONTIGHT THERMAL3.640.87
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 316 -
Rwork0.308 6007 -
all-6323 -
obs--98.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7395-0.12640.29450.50720.08852.4691-0.0396-0.03790.1377-0.0223-0.01230.2075-0.30630.01580.05180.0755-0.026-0.03310.0264-0.00250.1488-1.13530.228931.9442
20.3037-0.2360.29140.6863-0.42991.4705-0.0544-0.08040.0711-0.02390.0064-0.1174-0.15330.08920.0480.0492-0.04240.00450.1927-0.00410.07626.7031-6.123842.8769
31.35610.28720.64970.67860.38060.79240.0526-0.2338-0.16080.05360.01930.01990.10710.0383-0.07190.0512-0.02370.00460.16630.04750.053441.5852-28.997232.9709
42.07240.02830.76310.62840.01911.30660.09690.0517-0.1999-0.2712-0.0311-0.09820.24170.0586-0.06580.18840.01240.00970.01140.01220.060442.2199-35.38923.1414
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 306
2X-RAY DIFFRACTION2B5 - 306
3X-RAY DIFFRACTION3C5 - 306
4X-RAY DIFFRACTION4D5 - 306

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