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- PDB-6bpy: Aspergillus fumigatus Thioredoxin Reductase -

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Basic information

Entry
Database: PDB / ID: 6bpy
TitleAspergillus fumigatus Thioredoxin Reductase
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / redox homeostasis / Rossmann fold / dithiol
Function / homology
Function and homology information


thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADP) 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
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / FORMIC ACID / MALONATE ION / D-MALATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Thioredoxin reductase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.201 Å
AuthorsMarshall, A.C. / Bruning, J.B.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2019
Title: Structure, Mechanism, and Inhibition ofAspergillus fumigatusThioredoxin Reductase.
Authors: Marshall, A.C. / Kidd, S.E. / Lamont-Friedrich, S.J. / Arentz, G. / Hoffmann, P. / Coad, B.R. / Bruning, J.B.
History
DepositionNov 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)83,92220
Polymers79,8382
Non-polymers4,08318
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12330 Å2
ΔGint-20 kcal/mol
Surface area24960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.220, 159.220, 121.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 36 or resid 44...
21(chain B and ((resid 2 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLEULEU(chain A and (resid 2 through 36 or resid 44...AA2 - 363 - 37
12GLYGLYGLYGLY(chain A and (resid 2 through 36 or resid 44...AA4445
13GLNGLNGLNGLN(chain A and (resid 2 through 36 or resid 44...AA4546
14VALVALSERSER(chain A and (resid 2 through 36 or resid 44...AA2 - 3263 - 327
15VALVALSERSER(chain A and (resid 2 through 36 or resid 44...AA2 - 3263 - 327
16VALVALSERSER(chain A and (resid 2 through 36 or resid 44...AA2 - 3263 - 327
17VALVALSERSER(chain A and (resid 2 through 36 or resid 44...AA2 - 3263 - 327
21VALVALVALVAL(chain B and ((resid 2 and (name N or name...BB23
22METMETSERSER(chain B and ((resid 2 and (name N or name...BB1 - 3262 - 327
23METMETSERSER(chain B and ((resid 2 and (name N or name...BB1 - 3262 - 327
24METMETSERSER(chain B and ((resid 2 and (name N or name...BB1 - 3262 - 327
25METMETSERSER(chain B and ((resid 2 and (name N or name...BB1 - 3262 - 327

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thioredoxin reductase /


Mass: 39919.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (mold) / Gene: CDV57_04819, CDV58_04527 / Plasmid: pET-57-DEST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A229Y1X4, thioredoxin-disulfide reductase

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Non-polymers , 7 types, 63 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-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 5.56 Å3/Da / Density % sol: 77.89 % / Mosaicity: 1.33 °
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7 / Details: 32% Tacsimate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 7, 2015
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.2→29.97 Å / Num. obs: 28434 / % possible obs: 95.9 % / Redundancy: 12.3 % / Biso Wilson estimate: 92.69 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.055 / Rrim(I) all: 0.199 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.2-3.398.22.30942080.4410.7922.45188.9
9.6-29.9718.30.06611530.9990.0160.06896.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.98 Å60.06 Å
Translation7.98 Å60.06 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.17data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D8X
Resolution: 3.201→29.97 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.33
RfactorNum. reflection% reflection
Rfree0.2613 1407 4.99 %
Rwork0.231 --
obs0.2325 28215 95.29 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 207.86 Å2 / Biso mean: 26.0896 Å2 / Biso min: 1.95 Å2
Refinement stepCycle: final / Resolution: 3.201→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4721 0 237 45 5003
Biso mean--143.52 76.16 -
Num. residues----643
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2663X-RAY DIFFRACTION11.736TORSIONAL
12B2663X-RAY DIFFRACTION11.736TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2006-3.31490.39331260.37212390251686
3.3149-3.44740.37681290.33192509263890
3.4474-3.60410.34561280.32422509263791
3.6041-3.79380.30441360.28852611274794
3.7938-4.03090.26351360.26242681281796
4.0309-4.34130.31480.24012767291598
4.3413-4.77660.23421470.20672776292399
4.7766-5.46420.26311490.19982797294699
5.4642-6.87060.23291500.207828412991100
6.8706-29.9750.20411580.184129273085100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.2306-1.8344-2.25564.4511-3.04547.19470.6779-0.7498-1.41570.19-0.8226-0.83580.93880.65080.40030.9182-0.3267-0.13170.84290.24591.1938-52.975130.0394-43.0181
25.84811.13320.43796.34192.02799.48530.3929-0.2042-0.97820.058-0.3453-0.90451.9031-0.49950.03860.8837-0.0976-0.04720.73230.05310.9698-65.263425.7895-59.263
34.3024-0.1596-0.52673.778-1.47228.2380.717-1.3522-0.85620.7588-0.4422-1.23540.63071.0126-0.14441.0544-0.3187-0.26130.9510.35971.3531-50.921124.7465-39.355
43.47133.70511.96844.04092.7192.4033-0.0766-0.3404-0.69690.546-0.2061-0.7296-0.02090.80560.29561.1409-0.2249-0.28570.5840.20421.1557-68.123817.0743-49.8542
55.0039-0.2188-3.00355.85930.02715.31790.09360.21260.4489-0.21570.30230.4147-0.2322-0.2553-0.30620.8029-0.2047-0.21880.40360.18350.9807-84.728210.785-52.8842
62.01541.0802-0.07372.81441.92231.53340.9773-1.4996-0.3531.135-0.9510.51840.7-0.7920.02731.3322-0.5094-0.01510.95140.22950.9765-71.002621.6425-38.2616
75.4399-1.54243.1082.35121.05846.09711.0352-1.3365-0.21240.7716-0.5851-0.1425-0.1036-0.0631-0.31871.0972-0.42990.13830.78610.11580.7397-63.669536.2124-38.3438
83.0812-3.74171.15035.6172-0.66972.7790.14850.7951.3492-0.4938-0.00590.4084-0.0988-0.1267-0.14280.9696-0.2080.00380.68750.28910.9943-76.103644.1492-62.3124
98.17034.846-1.01295.5831-0.82490.74770.3892-0.60491.27160.7675-0.18440.8136-0.38780.0333-0.23940.9872-0.25040.11490.62890.02090.8871-61.173454.9625-49.0495
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 44 )A2 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 63 )A45 - 63
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 112 )A64 - 112
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 155 )A113 - 155
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 246 )A156 - 246
6X-RAY DIFFRACTION6chain 'A' and (resid 247 through 278 )A247 - 278
7X-RAY DIFFRACTION7chain 'A' and (resid 279 through 326 )A279 - 326
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 112 )B1 - 112
9X-RAY DIFFRACTION9chain 'B' and (resid 113 through 326 )B113 - 326

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