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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 / homologyin:ipr000103: / Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain superfamily / Pyridine nucleotide-disulphide oxidoreductase / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / thioredoxin-disulfide reductase / thioredoxin-disulfide reductase activity / removal of superoxide radicals ...in:ipr000103: / Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain superfamily / Pyridine nucleotide-disulphide oxidoreductase / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / thioredoxin-disulfide reductase / thioredoxin-disulfide reductase activity / removal of superoxide radicals / cytoplasm / Thioredoxin reductase
Function and homology information
Specimen sourceNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / 3.201 Å resolution
AuthorsMarshall, A.C. / Bruning, J.B.
CitationJournal: To be published
Title: Inhibition of Aspergillus fumigatus thioredoxin reductase by ebselen: a potential antifungal drug
Authors: Marshall, A.C. / Bruning, J.B.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 27, 2017 / Release: Jan 9, 2019

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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
Polyers79,8382
Non-polymers4,08318
Water81145
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)12330
ΔGint (kcal/M)-20
Surface area (Å2)24960
MethodPISA
Unit cell
γ
α
β
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-MP 32 2 1

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Components

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Protein/peptide , 1 types, 2 molecules AB

#1: Protein/peptide Thioredoxin reductase /


Mass: 39919.066 Da / Num. of mol.: 2 / Source: (gene. exp.) Neosartorya fumigata (mold) / Gene: CDV57_04819, CDV58_04527 / Plasmid name: 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


Mass: 785.550 Da / Num. of mol.: 2 / Formula: C27H33N9O15P2 / Flavin adenine dinucleotide / Comment: FAD *YM
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 5 / Formula: C3H2O4 / Malonate
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Formula: CH2O2 / Formic acid
#5: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Formula: C21H28N7O17P3 / Nicotinamide adenine dinucleotide phosphate
#6: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 134.087 Da / Num. of mol.: 1 / Formula: C4H6O5 / Malic acid
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Formula: H2O / Water

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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 / Density percent sol: 77.89 % / Mosaicity: 1.33 deg.
Crystal growTemp: 289 K / Method: vapor diffusion / pH: 7 / Details: 32% Tacsimate

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: AUSTRALIAN SYNCHROTRON BEAMLINE MX1 / Synchrotron site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Collection date: Aug 7, 2015
RadiationMonochromator: Silicon Double Crystal / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 92.69 Å2 / D resolution high: 3.2 Å / D resolution low: 29.97 Å / Number obs: 28434 / CC half: 0.994 / Rmerge I obs: 0.191 / Rpim I all: 0.055 / Rrim I all: 0.199 / NetI over sigmaI: 9.4 / Redundancy: 12.3 % / Percent possible obs: 95.9
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionNumber unique obsCC halfRpim I allRrim I allRedundancyPercent possible all
2.3093.2003.39042080.4410.7922.4518.20088.900
0.0669.60029.97011530.9990.0160.06818.30096.700

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Phasing

PhasingMethod: molecular replacement
Phasing MRD res high rotation: 7.98 / D res high translation: 7.98 / D res low rotation: 60.06 / D res low translation: 60.06 / Model details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationContact authorContact author emailLocationTypeDateLanguage
MOSFLMdata reductionAndrew G.W. Leslieandrew[at]mrc-lmb.cam.ac.ukhttp://www.mrc-lmb.cam.ac.uk/harry/mosflm/package
Aimless0.5.17data scalingPhil Evanshttp://www.mrc-lmb.cam.ac.uk/harry/pre/aimless.htmlprogram21/10/15
PHASER2.5.6phasingRandy J. Readcimr-phaser[at]lists.cam.ac.ukhttp://www-structmed.cimr.cam.ac.uk/phaser/programTue Dec 02 00:01:53 2014
PHENIXrefinementPaul D. AdamsPDAdams[at]lbl.govhttp://www.phenix-online.org/packageC++
PDB_EXTRACT3.24data extractionPDBdeposit[at]deposit.rcsb.orghttp://sw-tools.pdb.org/apps/PDB_EXTRACT/packageSep. 1, 2017C++
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D8X

3d8x


Overall SU ML: 0.46 / Cross valid method: THROUGHOUT / Sigma F: 1.33 / Overall phase error: 29.33
Solvent computationSolvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.1 Å
Displacement parametersB iso max: 207.86 Å2 / B iso mean: 26.0896 Å2 / B iso min: 1.95 Å2
Least-squares processR factor R free: 0.2613 / R factor R work: 0.231 / R factor obs: 0.2325 / Highest resolution: 3.201 Å / Lowest resolution: 29.97 Å / Number reflection R free: 1407 / Number reflection obs: 28215 / Percent reflection R free: 4.99 / Percent reflection obs: 95.29
Refine hist #finalHighest resolution: 3.201 Å / Lowest resolution: 29.97 Å / B iso mean ligand: 143.52 / B iso mean solvent: 76.16 / Number residues total: 643
Number of atoms included #finalProtein: 4721 / Nucleic acid: 0 / Ligand: 237 / Solvent: 45 / Total: 5003
Refine LS restraints ncs

Ens ID: 1 / Number: 2663 / Refine ID: X-RAY DIFFRACTION / Rms: 11.736 / Type: TORSIONAL

Dom IDAuth asym ID
1A
2B
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 10

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
3.20060.39330.37213.31491262390251686.0000
3.31490.37680.33193.44741292509263890.0000
3.44740.34560.32423.60411282509263791.0000
3.60410.30440.28853.79381362611274794.0000
3.79380.26350.26244.03091362681281796.0000
4.03090.30000.24014.34131482767291598.0000
4.34130.23420.20674.77661472776292399.0000
4.77660.26310.19985.46421492797294699.0000
5.46420.23290.20786.870615028412991100.0000
6.87060.20410.184129.975015829273085100.0000
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
13.2306-1.8344-2.25564.4511-3.04547.19470.6779-0.7498-1.41570.1900-0.8226-0.83580.93880.65080.40030.9182-0.3267-0.13170.84290.24591.1938-52.975130.0394-43.0181
25.84811.13320.43796.34192.02799.48530.3929-0.2042-0.97820.0580-0.3453-0.90451.9031-0.49950.03860.8837-0.0976-0.04720.73230.05310.9698-65.263425.7895-59.2630
34.3024-0.1596-0.52673.7780-1.47228.23800.7170-1.3522-0.85620.7588-0.4422-1.23540.63071.0126-0.14441.0544-0.3187-0.26130.95100.35971.3531-50.921124.7465-39.3550
43.47133.70511.96844.04092.71902.4033-0.0766-0.3404-0.69690.5460-0.2061-0.7296-0.02090.80560.29561.1409-0.2249-0.28570.58400.20421.1557-68.123817.0743-49.8542
55.0039-0.2188-3.00355.85930.02715.31790.09360.21260.4489-0.21570.30230.4147-0.2322-0.2553-0.30620.8029-0.2047-0.21880.40360.18350.9807-84.728210.7850-52.8842
62.01541.0802-0.07372.81441.92231.53340.9773-1.4996-0.35301.1350-0.95100.51840.7000-0.79200.02731.3322-0.5094-0.01510.95140.22950.9765-71.002621.6425-38.2616
75.4399-1.54243.10802.35121.05846.09711.0352-1.3365-0.21240.7716-0.5851-0.1425-0.1036-0.0631-0.31871.0972-0.42990.13830.78610.11580.7397-63.669536.2124-38.3438
83.0812-3.74171.15035.6172-0.66972.77900.14850.79501.3492-0.4938-0.00590.4084-0.0988-0.1267-0.14280.9696-0.20800.00380.68750.28910.9943-76.103644.1492-62.3124
98.17034.8460-1.01295.5831-0.82490.74770.3892-0.60491.27160.7675-0.18440.8136-0.38780.0333-0.23940.9872-0.25040.11490.62890.02090.8871-61.173454.9625-49.0495
Refine TLS group

Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDEnd auth asym IDEnd auth seq IDRefine TLS IDSelection details
1A2A441chain 'A' and (resid 2 through 44 )
2A45A632chain 'A' and (resid 45 through 63 )
3A64A1123chain 'A' and (resid 64 through 112 )
4A113A1554chain 'A' and (resid 113 through 155 )
5A156A2465chain 'A' and (resid 156 through 246 )
6A247A2786chain 'A' and (resid 247 through 278 )
7A279A3267chain 'A' and (resid 279 through 326 )
8B1B1128chain 'B' and (resid 1 through 112 )
9B113B3269chain 'B' and (resid 113 through 326 )

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