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- PDB-6a4j: Crystal structure of Thioredoxin reductase 2 from Staphylococcus ... -

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Basic information

Entry
Database: PDB / ID: 6a4j
TitleCrystal structure of Thioredoxin reductase 2 from Staphylococcus aureus
ComponentsFerredoxin--NADP reductase
KeywordsOXIDOREDUCTASE / flavoenzyme
Function / homology
Function and homology information


ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / monooxygenase activity / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
Ferredoxin--NADP reductase, type 2 / 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 / Ferredoxin--NADP reductase / Ferredoxin--NADP reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBose, M. / Bhattacharyya, S. / Ghosh, A.K. / Das, A.K.
Funding support India, 1items
OrganizationGrant numberCountry
BT/326/NE/TBP/2012, Dated: 06-12-2012 India
CitationJournal: Biochimie / Year: 2019
Title: Elucidation of the mechanism of disulfide exchange between staphylococcal thioredoxin2 and thioredoxin reductase2: A structural insight.
Authors: Bose, M. / Bhattacharyya, S. / Biswas, R. / Roychowdhury, A. / Bhattacharjee, A. / Ghosh, A.K. / Das, A.K.
History
DepositionJun 20, 2018Deposition site: PDBJ / Processing site: PDBJ
SupersessionJul 11, 2018ID: 5ZBV
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Nov 22, 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

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Assembly

Deposited unit
A: Ferredoxin--NADP reductase
B: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1484
Polymers76,5772
Non-polymers1,5712
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8750 Å2
ΔGint-58 kcal/mol
Surface area26970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.614, 90.934, 141.458
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ferredoxin--NADP reductase / thioredoxin reductase / Fd-NADP(+) reductase


Mass: 38288.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: trxB_2, EP54_04310, EQ90_00075, RK60_12235, RK64_12650, RK68_02995, RK73_09520, RK98_08250, RL06_05030, SAMEA3448991_00661
Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009
References: UniProt: A0A1Q4GXS1, UniProt: Q2FVP8*PLUS, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C27H33N9O15P2 / Comment: FAD*YM

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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: 3.3 Å3/Da / Density % sol: 62.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4 M sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 28, 2017 / Details: varimax osmic mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→19.861 Å / Num. obs: 14419 / % possible obs: 99.3 % / Redundancy: 2 % / CC1/2: 0.979 / Rmerge(I) obs: 0.1193 / Rpim(I) all: 0.1193 / Rrim(I) all: 0.1687 / Net I/σ(I): 6.01
Reflection shellResolution: 3.4→19.86 Å / Rmerge(I) obs: 0.3953 / Num. unique obs: 1427 / CC1/2: 0.658 / Rpim(I) all: 0.3953 / Rrim(I) all: 0.559

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TWC

5twc


Resolution: 3.4→19.861 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.56
RfactorNum. reflection% reflection
Rfree0.2666 733 5.08 %
Rwork0.2411 --
obs0.2426 14416 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.4→19.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5137 0 106 0 5243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045355
X-RAY DIFFRACTIONf_angle_d0.9317292
X-RAY DIFFRACTIONf_dihedral_angle_d8.6473100
X-RAY DIFFRACTIONf_chiral_restr0.058841
X-RAY DIFFRACTIONf_plane_restr0.003913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.6610.28891560.28842672X-RAY DIFFRACTION100
3.661-4.02670.3151390.25322698X-RAY DIFFRACTION100
4.0267-4.6030.27121400.22212730X-RAY DIFFRACTION100
4.603-5.77560.22951490.23552726X-RAY DIFFRACTION100
5.7756-19.86090.25611490.23062857X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -4.6846 Å / Origin y: 16.8835 Å / Origin z: -53.5689 Å
111213212223313233
T0.2513 Å2-0.0415 Å2-0.0178 Å2-0.2208 Å2-0.0441 Å2--0.2764 Å2
L0.6402 °2-0.1631 °20.1406 °2-0.2802 °2-0.2258 °2--0.698 °2
S0.0712 Å °0.0397 Å °-0.0838 Å °-0.0062 Å °-0.0283 Å °0.0374 Å °0.0261 Å °-0.0859 Å °-0 Å °
Refinement TLS groupSelection details: all

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