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- PDB-5uth: Crystal structure of thioredoxin reductase from Mycobacterium sme... -

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Basic information

Entry
Database: PDB / ID: 5uth
TitleCrystal structure of thioredoxin reductase from Mycobacterium smegmatis in complex with FAD
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / SSGCID / Mycobacerium smegmatis / thiredoxin reductase / FAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of thioredoxin reductase from Mycobacterium smegmatis in complex with FAD
Authors: Abendroth, J. / Irwin, R.M. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionFeb 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Other
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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,32512
Polymers34,5791
Non-polymers1,74611
Water5,368298
1
A: Thioredoxin reductase
hetero molecules

A: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,65024
Polymers69,1572
Non-polymers3,49222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area10970 Å2
ΔGint-232 kcal/mol
Surface area24900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.280, 69.280, 153.800
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-718-

HOH

21A-781-

HOH

31A-798-

HOH

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Components

#1: Protein Thioredoxin reductase /


Mass: 34578.730 Da / Num. of mol.: 1 / Fragment: MysmA.00058.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: trxB, MSMEG_6933, MSMEI_6742 / Plasmid: MysmA.00058.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0R7I9, thioredoxin-disulfide reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 3.09 Å3/Da / Density % sol: 60.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: AnatraceTop96 screen, E1: 2M Ammonium sulfate, 100mM BisTris pH 5.5: MysmA.00058.a.B1.PS38133 at 22.8mg/ml + 3mM NADP. Over night soak with 5x drop volume of FAD in reservoir: cryo: 3M ...Details: AnatraceTop96 screen, E1: 2M Ammonium sulfate, 100mM BisTris pH 5.5: MysmA.00058.a.B1.PS38133 at 22.8mg/ml + 3mM NADP. Over night soak with 5x drop volume of FAD in reservoir: cryo: 3M Ammonium sulfate; tray 248209h3, puck xtp3-5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 22, 2009
RadiationMonochromator: Rigaku VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→38.976 Å / Num. obs: 31655 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 9.399 % / Biso Wilson estimate: 26.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.062 / Χ2: 1.056 / Net I/σ(I): 24.69
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allNum. unique obsCC1/2Rrim(I) all% possible all
1.95-24.3980.3983.27215421540.9370.45293.7
2-2.065.4970.3154.8122410.9660.34898.7
2.06-2.127.1340.2766.7822160.980.29899.9
2.12-2.189.8990.2289.6121350.9920.2499.9
2.18-2.259.8560.24311.0620320.9920.25797
2.25-2.3310.1210.19613.2119140.9960.20794.9
2.33-2.4210.70.14814.9219380.9970.156100
2.42-2.5210.70.13116.4918840.9970.13799.8
2.52-2.6310.7210.11218.918060.9980.117100
2.63-2.7610.7420.09322.3517420.9990.097100
2.76-2.9110.7520.07726.8316600.9990.081100
2.91-3.0810.7790.06332.6415540.9990.066100
3.08-3.310.6740.04941.9914860.9990.051100
3.3-3.5610.4690.04447.5513680.9990.046100
3.56-3.99.8540.03953.4812850.9990.04299.7
3.9-4.3610.2310.03359.47117210.035100
4.36-5.0310.3380.0363.09103310.03199.8
5.03-6.1710.4340.03155.8589210.03399.9
6.17-8.7210.0720.02859.4271810.029100
8.72-508.8870.02167.1842510.02297

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å38.98 Å
Translation2 Å38.98 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
PDB_EXTRACT3.22data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2a87 as found by morda

2a87


Resolution: 1.95→38.976 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.92
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 1937 6.13 %0
Rwork0.167 ---
obs0.1691 31595 98.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.28 Å2 / Biso mean: 35.5459 Å2 / Biso min: 12.73 Å2
Refinement stepCycle: final / Resolution: 1.95→38.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2258 0 103 301 2662
Biso mean--42.63 41.88 -
Num. residues----306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062440
X-RAY DIFFRACTIONf_angle_d0.8023340
X-RAY DIFFRACTIONf_chiral_restr0.056379
X-RAY DIFFRACTIONf_plane_restr0.006467
X-RAY DIFFRACTIONf_dihedral_angle_d14.4871447
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9501-1.99880.26731330.20981943207694
1.9988-2.05290.22611340.18792085221998
2.0529-2.11330.23651440.18521062250100
2.1133-2.18150.21931120.176321122224100
2.1815-2.25940.3271230.25682074219797
2.2594-2.34990.25721310.18572034216595
2.3499-2.45680.21211580.167420952253100
2.4568-2.58630.23131210.174421292250100
2.5863-2.74830.19311310.169821462277100
2.7483-2.96050.20531310.175321562287100
2.9605-3.25830.20611840.173921012285100
3.2583-3.72940.20481390.154121732312100
3.7294-4.69740.1511640.12621732337100
4.6974-38.98380.1771320.164123312463100
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)
11.1974-0.3867-0.3662.37121.10522.48940.0568-0.09560.04920.17970.0658-0.1472-0.08850.2377-0.13380.1253-0.03220.00510.2193-0.02280.143122.77729.1791-13.4229
20.9095-2.21621.02957.7025-4.03113.1878-0.0338-0.1444-0.02160.48680.1564-0.0459-0.05180.1065-0.14440.22460.0148-0.00790.2709-0.00930.193817.0287-1.8182-6.6309
30.86260.0003-0.85064.0456-2.59614.0061-0.29370.1127-0.0685-0.42690.44320.15080.5488-0.2473-0.0930.34270.0057-0.02320.38910.0570.271417.518-24.0484-8.8071
40.9407-0.5185-0.32232.5125-0.46871.70830.0155-0.0575-0.05140.17370.06320.2746-0.0798-0.1693-0.09270.1133-0.00450.01670.2256-0.00020.15729.87032.0944-15.3944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 107 )A5 - 107
2X-RAY DIFFRACTION2chain 'A' and (resid 108 through 128 )A108 - 128
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 231 )A129 - 231
4X-RAY DIFFRACTION4chain 'A' and (resid 232 through 310 )A232 - 310

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