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- PDB-5usx: Crystal structure of thioredoxin-disulfide reductase from Vibrio ... -

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Basic information

Entry
Database: PDB / ID: 5usx
TitleCrystal structure of thioredoxin-disulfide reductase from Vibrio vulnificus CMCP6 in complex with NADP and FAD
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center For Structural Genomics Of Infectious Diseases / CSGID / thioredoxin-disulfide reductase
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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Thioredoxin reductase
Similarity search - Component
Biological speciesVibrio vulnificus CMCP6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å
AuthorsChang, C. / Grimshaw, S. / Maltseva, N. / Mulligan, R. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of thioredoxin-disulfide reductase from Vibrio vulnificus CMCP6 in complex with NADP and FAD
Authors: Chang, C. / Grimshaw, S. / Maltseva, N. / Mulligan, R. / Anderson, W.F. / Joachimiak, A.
History
DepositionFeb 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
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
B: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9478
Polymers68,7652
Non-polymers3,1826
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10910 Å2
ΔGint-22 kcal/mol
Surface area24630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.626, 98.302, 119.879
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thioredoxin reductase / thioredoxin-disulfide reductase


Mass: 34382.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus CMCP6 (bacteria) / Gene: VV1455
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q7MLH2, thioredoxin-disulfide reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN SEQUENCE MATCHES TO GENBANK 27366093.

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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: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 80 mM potassium chloride, 40 mM sodium cacodylate, 55% MPD, 12 mM spermidine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 30, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 24042 / % possible obs: 99.1 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 17
Reflection shellHighest resolution: 2.6 Å

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Processing

Software
NameVersionClassification
PHENIXdev_2614refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CL0

1cl0


Resolution: 2.603→40.12 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.55
RfactorNum. reflection% reflection
Rfree0.2328 1211 5.15 %
Rwork0.1868 --
obs0.1893 23503 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.53 Å2 / Biso mean: 48.9252 Å2 / Biso min: 9.2 Å2
Refinement stepCycle: final / Resolution: 2.603→40.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4736 0 210 118 5064
Biso mean--54.77 41.2 -
Num. residues----630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025055
X-RAY DIFFRACTIONf_angle_d0.5926872
X-RAY DIFFRACTIONf_chiral_restr0.043770
X-RAY DIFFRACTIONf_plane_restr0.002874
X-RAY DIFFRACTIONf_dihedral_angle_d15.092961
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6026-2.70680.30071020.24132042214481
2.7068-2.830.27351220.23192477259999
2.83-2.97910.3111430.233424972640100
2.9791-3.16570.29891220.211825192641100
3.1657-3.410.24711430.19632500264399
3.41-3.7530.21551380.182625122650100
3.753-4.29550.21721470.15842531267899
4.2955-5.40980.18821660.157725392705100
5.4098-40.12510.21991280.18482675280399
Refinement TLS params.Method: refined / Origin x: 23.2553 Å / Origin y: 15.3494 Å / Origin z: 23.7868 Å
111213212223313233
T0.1112 Å2-0.0131 Å2-0.0215 Å2-0.1282 Å20.0319 Å2--0.1012 Å2
L0.254 °2-0.0485 °2-0.434 °2-0.4954 °20.3909 °2--0.4129 °2
S0.0379 Å °-0.0437 Å °-0.0151 Å °0.0464 Å °0.001 Å °-0.0441 Å °0.1034 Å °-0.0368 Å °0.0098 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 317
2X-RAY DIFFRACTION1allB4 - 317
3X-RAY DIFFRACTION1allD1 - 2
4X-RAY DIFFRACTION1allE1 - 2
5X-RAY DIFFRACTION1allS1 - 118
6X-RAY DIFFRACTION1allC1 - 2

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