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- PDB-7a76: Bacillithiol Disulfide Reductase Bdr (YpdA) from Bacillus cereus -

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Basic information

Entry
Database: PDB / ID: 7a76
TitleBacillithiol Disulfide Reductase Bdr (YpdA) from Bacillus cereus
ComponentsTHIOREDOXIN REDUCTASE
KeywordsOXIDOREDUCTASE / disulfide reductase / FAD / flavoprotein / NADPH
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / monooxygenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Bacilliredoxin reductase Bdr / Pyridine nucleotide-disulphide oxidoreductase / : / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin reductase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHammerstad, M. / Gudim, I. / Hersleth, H.-P.
Funding support Norway, 2items
OrganizationGrant numberCountry
Research Council of Norway231669 Norway
Research Council of Norway301584 Norway
CitationJournal: Biochemistry / Year: 2020
Title: The Crystal Structures of Bacillithiol Disulfide Reductase Bdr (YpdA) Provide Structural and Functional Insight into a New Type of FAD-Containing NADPH-Dependent Oxidoreductase.
Authors: Hammerstad, M. / Gudim, I. / Hersleth, H.P.
History
DepositionAug 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 13, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3May 1, 2024Group: 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
C: THIOREDOXIN REDUCTASE
D: THIOREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,33512
Polymers146,1014
Non-polymers3,2348
Water15,439857
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, DLS, Native PAGE
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15860 Å2
ΔGint-113 kcal/mol
Surface area52830 Å2
Unit cell
Length a, b, c (Å)88.731, 114.900, 146.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein
THIOREDOXIN REDUCTASE


Mass: 36525.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria)
Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711
Gene: BC_1495 / Production host: Escherichia coli (E. coli)
References: UniProt: Q81FS4, thioredoxin-disulfide reductase (NADPH)
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 857 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris, pH = 7.0, 10% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.65→73.4 Å / Num. obs: 175671 / % possible obs: 97.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 27.09 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.086 / Net I/σ(I): 10
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.81 / Num. unique obs: 8583 / CC1/2: 0.728 / Rrim(I) all: 0.915 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
REFMAC5.8.0253refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3.5 A SELENO-SAD BCYPDA MODEL

Resolution: 1.65→45.23 Å / SU ML: 0.1819 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.9649
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2182 8787 5.01 %
Rwork0.1898 166770 -
obs0.1912 175557 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.52 Å2
Refinement stepCycle: LAST / Resolution: 1.65→45.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10276 0 216 857 11349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006111161
X-RAY DIFFRACTIONf_angle_d0.817115213
X-RAY DIFFRACTIONf_chiral_restr0.05841645
X-RAY DIFFRACTIONf_plane_restr0.00471985
X-RAY DIFFRACTIONf_dihedral_angle_d15.70024075
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.3143050.27075464X-RAY DIFFRACTION97.63
1.67-1.690.29152920.25785465X-RAY DIFFRACTION97
1.69-1.710.29413040.25425486X-RAY DIFFRACTION97.38
1.71-1.730.26542970.24215493X-RAY DIFFRACTION97.67
1.73-1.750.26282910.23375483X-RAY DIFFRACTION97.53
1.75-1.780.26192880.23085565X-RAY DIFFRACTION97.75
1.78-1.80.25762710.2295305X-RAY DIFFRACTION93.84
1.8-1.830.26412360.22065272X-RAY DIFFRACTION92.63
1.83-1.860.26893120.22435535X-RAY DIFFRACTION97.73
1.86-1.890.25422850.21565529X-RAY DIFFRACTION97.65
1.89-1.920.24583000.21315537X-RAY DIFFRACTION98.18
1.92-1.960.25612960.21365540X-RAY DIFFRACTION97.82
1.96-1.990.25422940.20825518X-RAY DIFFRACTION97.37
1.99-2.030.2462780.20275590X-RAY DIFFRACTION98.31
2.03-2.080.25652800.2095556X-RAY DIFFRACTION98.07
2.08-2.130.22842770.20255665X-RAY DIFFRACTION98.57
2.13-2.180.21172760.19345595X-RAY DIFFRACTION98.72
2.18-2.240.22442790.19995649X-RAY DIFFRACTION98.9
2.24-2.310.23062880.19845212X-RAY DIFFRACTION91.82
2.31-2.380.23873080.19735475X-RAY DIFFRACTION96.79
2.38-2.460.21232890.19095639X-RAY DIFFRACTION98.73
2.46-2.560.25013230.19895640X-RAY DIFFRACTION99.45
2.56-2.680.22983120.19915697X-RAY DIFFRACTION99.31
2.68-2.820.23242950.19695661X-RAY DIFFRACTION99.25
2.82-30.23343120.19795680X-RAY DIFFRACTION99.45
3-3.230.23553140.19855695X-RAY DIFFRACTION99.01
3.23-3.550.21082720.18715359X-RAY DIFFRACTION92.71
3.55-4.070.20373000.16835783X-RAY DIFFRACTION99.67
4.07-5.120.16593140.15355817X-RAY DIFFRACTION99.71
5.12-45.230.18622990.17755865X-RAY DIFFRACTION96.18
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)
10.334058853425-0.370148536120.4250412302561.19310189584-0.7264029383931.89112355005-0.0918227875062-0.1427322167010.04427843324270.3888656625750.09790386631420.177255723299-0.201244032445-0.305170401620.002892922750250.2262964491550.01374189872820.06968439933580.218576570185-0.014978024240.2082268040142.667166217826.441501191-16.8949953039
20.536308431237-0.1549687179950.2689359154851.86484274864-1.010391361322.142549736340.03786608627650.125075003197-0.163187668738-0.256654296356-0.0808935109-0.008819865498270.3939115720210.08298799924960.04167770539890.1926455622540.008534560988250.03359628840950.193583575781-0.03070122067940.22244552479555.59552434256.70969047455-42.0391012506
31.344719656910.0410493153804-0.7195292654941.973580405711.407248996162.905743641840.1512515950080.1828267795170.300782397916-0.482448794552-0.0139087428131-0.212385041372-0.743032261213-0.23579118735-0.09305905258440.3117035069320.04326490981020.07174846848950.1848740364610.05377778281680.2511596784474.72922823149.3436828623-39.8232860078
41.267591075640.644216241482-0.8604010451552.004308033320.1088052452082.119729195340.0369002554354-0.423213365754-0.4928944559330.564338631184-0.140633407605-0.9560403185430.303157224610.4859944309530.00182395374230.201706677340.0530499520278-0.1826731202050.3321139891290.1196813704960.59510129285689.119730080825.4407552217-20.0075713559
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:326)
2X-RAY DIFFRACTION2(chain B and resseq 1:326)
3X-RAY DIFFRACTION3(chain C and resseq 1:325)
4X-RAY DIFFRACTION4(chain D and resseq 2:325)

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