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- PDB-7a7b: Bacillithiol Disulfide Reductase Bdr (YpdA) from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 7a7b
TitleBacillithiol Disulfide Reductase Bdr (YpdA) from Staphylococcus aureus
ComponentsYpdA family putative bacillithiol disulfide reductase Bdr
KeywordsOXIDOREDUCTASE / disulfide reductase / FAD / flavoprotein / NADPH
Function / homologyBacilliredoxin reductase Bdr / Pyridine nucleotide-disulphide oxidoreductase / : / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / nucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pyridine nucleotide-disulfide oxidoreductase
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHammerstad, M. / 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 1.3Jan 31, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YpdA family putative bacillithiol disulfide reductase Bdr
B: YpdA family putative bacillithiol disulfide reductase Bdr
C: YpdA family putative bacillithiol disulfide reductase Bdr
D: YpdA family putative bacillithiol disulfide reductase Bdr
E: YpdA family putative bacillithiol disulfide reductase Bdr
F: YpdA family putative bacillithiol disulfide reductase Bdr
G: YpdA family putative bacillithiol disulfide reductase Bdr
H: YpdA family putative bacillithiol disulfide reductase Bdr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,72619
Polymers294,2118
Non-polymers8,51511
Water46826
1
A: YpdA family putative bacillithiol disulfide reductase Bdr
B: YpdA family putative bacillithiol disulfide reductase Bdr
C: YpdA family putative bacillithiol disulfide reductase Bdr
D: YpdA family putative bacillithiol disulfide reductase Bdr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,73510
Polymers147,1064
Non-polymers4,6296
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16380 Å2
ΔGint-73 kcal/mol
Surface area52810 Å2
MethodPISA
2
E: YpdA family putative bacillithiol disulfide reductase Bdr
F: YpdA family putative bacillithiol disulfide reductase Bdr
hetero molecules

E: YpdA family putative bacillithiol disulfide reductase Bdr
F: YpdA family putative bacillithiol disulfide reductase Bdr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,73510
Polymers147,1064
Non-polymers4,6296
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area16320 Å2
ΔGint-76 kcal/mol
Surface area53210 Å2
MethodPISA
3
G: YpdA family putative bacillithiol disulfide reductase Bdr
H: YpdA family putative bacillithiol disulfide reductase Bdr
hetero molecules

G: YpdA family putative bacillithiol disulfide reductase Bdr
H: YpdA family putative bacillithiol disulfide reductase Bdr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,2488
Polymers147,1064
Non-polymers3,1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_435x-y-1,-y-2,-z1
Buried area14260 Å2
ΔGint-72 kcal/mol
Surface area54550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.315, 179.315, 349.336
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETILEILE(chain 'A' and (resid 1 through 27 or resid 29...AA1 - 271 - 27
12THRTHRPHEPHE(chain 'A' and (resid 1 through 27 or resid 29...AA29 - 5029 - 50
13SERSERGLUGLU(chain 'A' and (resid 1 through 27 or resid 29...AA52 - 6752 - 67
14SERSERHISHIS(chain 'A' and (resid 1 through 27 or resid 29...AA69 - 8769 - 87
15LEULEUMETMET(chain 'A' and (resid 1 through 27 or resid 29...AA89 - 10389 - 103
16ASNASNGLNGLN(chain 'A' and (resid 1 through 27 or resid 29...AA105 - 323105 - 323
17FADFADFADFAD(chain 'A' and (resid 1 through 27 or resid 29...AI401
28METMETILEILE(chain 'B' and (resid 1 through 27 or resid 29...BB1 - 271 - 27
29THRTHRPHEPHE(chain 'B' and (resid 1 through 27 or resid 29...BB29 - 5029 - 50
210SERSERGLUGLU(chain 'B' and (resid 1 through 27 or resid 29...BB52 - 6752 - 67
211SERSERHISHIS(chain 'B' and (resid 1 through 27 or resid 29...BB69 - 8769 - 87
212LEULEUMETMET(chain 'B' and (resid 1 through 27 or resid 29...BB89 - 10389 - 103
213ASNASNGLNGLN(chain 'B' and (resid 1 through 27 or resid 29...BB105 - 323105 - 323
214FADFADFADFAD(chain 'B' and (resid 1 through 27 or resid 29...BJ401
315METMETILEILE(chain 'C' and (resid 1 through 27 or resid 29...CC1 - 271 - 27
316THRTHRPHEPHE(chain 'C' and (resid 1 through 27 or resid 29...CC29 - 5029 - 50
317SERSERGLUGLU(chain 'C' and (resid 1 through 27 or resid 29...CC52 - 6752 - 67
318SERSERHISHIS(chain 'C' and (resid 1 through 27 or resid 29...CC69 - 8769 - 87
319LEULEUMETMET(chain 'C' and (resid 1 through 27 or resid 29...CC89 - 10389 - 103
320ASNASNGLNGLN(chain 'C' and (resid 1 through 27 or resid 29...CC105 - 323105 - 323
321FADFADFADFAD(chain 'C' and (resid 1 through 27 or resid 29...CK401
422METMETILEILE(chain 'D' and (resid 1 through 27 or resid 29...DD1 - 271 - 27
423THRTHRPHEPHE(chain 'D' and (resid 1 through 27 or resid 29...DD29 - 5029 - 50
424SERSERGLUGLU(chain 'D' and (resid 1 through 27 or resid 29...DD52 - 6752 - 67
425SERSERHISHIS(chain 'D' and (resid 1 through 27 or resid 29...DD69 - 8769 - 87
426LEULEUMETMET(chain 'D' and (resid 1 through 27 or resid 29...DD89 - 10389 - 103
427ASNASNGLNGLN(chain 'D' and (resid 1 through 27 or resid 29...DD105 - 323105 - 323
428FADFADFADFAD(chain 'D' and (resid 1 through 27 or resid 29...DM401
529METMETILEILE(chain 'E' and (resid 1 through 27 or resid 29...EE1 - 271 - 27
530THRTHRPHEPHE(chain 'E' and (resid 1 through 27 or resid 29...EE29 - 5029 - 50
531SERSERGLUGLU(chain 'E' and (resid 1 through 27 or resid 29...EE52 - 6752 - 67
532SERSERHISHIS(chain 'E' and (resid 1 through 27 or resid 29...EE69 - 8769 - 87
533LEULEUMETMET(chain 'E' and (resid 1 through 27 or resid 29...EE89 - 10389 - 103
534ASNASNGLNGLN(chain 'E' and (resid 1 through 27 or resid 29...EE105 - 323105 - 323
535FADFADFADFAD(chain 'E' and (resid 1 through 27 or resid 29...EO401
636METMETILEILE(chain 'F' and (resid 1 through 27 or resid 29...FF1 - 271 - 27
637THRTHRPHEPHE(chain 'F' and (resid 1 through 27 or resid 29...FF29 - 5029 - 50
638SERSERGLUGLU(chain 'F' and (resid 1 through 27 or resid 29...FF52 - 6752 - 67
639SERSERHISHIS(chain 'F' and (resid 1 through 27 or resid 29...FF69 - 8769 - 87
640LEULEUMETMET(chain 'F' and (resid 1 through 27 or resid 29...FF89 - 10389 - 103
641ASNASNGLNGLN(chain 'F' and (resid 1 through 27 or resid 29...FF105 - 323105 - 323
642FADFADFADFAD(chain 'F' and (resid 1 through 27 or resid 29...FP401
743METMETILEILE(chain 'H' and (resid 1 through 27 or resid 29...HH1 - 271 - 27
744THRTHRPHEPHE(chain 'H' and (resid 1 through 27 or resid 29...HH29 - 5029 - 50
745SERSERGLUGLU(chain 'H' and (resid 1 through 27 or resid 29...HH52 - 6752 - 67
746SERSERHISHIS(chain 'H' and (resid 1 through 27 or resid 29...HH69 - 8769 - 87
747LEULEUMETMET(chain 'H' and (resid 1 through 27 or resid 29...HH89 - 10389 - 103
748ASNASNGLNGLN(chain 'H' and (resid 1 through 27 or resid 29...HH105 - 323105 - 323
749FADFADFADFAD(chain 'H' and (resid 1 through 27 or resid 29...HS401

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Components

#1: Protein
YpdA family putative bacillithiol disulfide reductase Bdr


Mass: 36776.434 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain COL) (bacteria)
Strain: COL / Gene: SACOL1520 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2WWS2
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.8 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.1 M MOPS/HEPES-Na, pH = 7.5, 10% w/v PEG 4000, 20% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1.49379 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.49379 Å / Relative weight: 1
ReflectionResolution: 2.9→49.63 Å / Num. obs: 73800 / % possible obs: 99.8 % / Redundancy: 18 % / Biso Wilson estimate: 59.42 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.169 / Rrim(I) all: 0.165 / Net I/σ(I): 13.9
Reflection shellResolution: 2.9→2.96 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 4449 / CC1/2: 0.951 / Rrim(I) all: 0.565

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7A76

7a76


Resolution: 2.9→49.63 Å / SU ML: 0.4445 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.2821
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3077 3682 4.99 %
Rwork0.2433 70063 -
obs0.2465 73745 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.44 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19991 0 568 26 20585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009421140
X-RAY DIFFRACTIONf_angle_d1.203128773
X-RAY DIFFRACTIONf_chiral_restr0.06933166
X-RAY DIFFRACTIONf_plane_restr0.00773623
X-RAY DIFFRACTIONf_dihedral_angle_d20.99677573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.940.37491370.272634X-RAY DIFFRACTION99.11
2.94-2.980.4021180.24762641X-RAY DIFFRACTION99.39
2.98-3.020.33111260.23852668X-RAY DIFFRACTION99.36
3.02-3.070.29991470.23182601X-RAY DIFFRACTION99.21
3.07-3.110.32981340.24362671X-RAY DIFFRACTION99.5
3.11-3.160.33951400.24842645X-RAY DIFFRACTION99.57
3.17-3.220.34811300.25272653X-RAY DIFFRACTION99.39
3.22-3.280.35021550.26972609X-RAY DIFFRACTION99.42
3.28-3.340.36431350.25172690X-RAY DIFFRACTION99.61
3.34-3.410.30981420.2452649X-RAY DIFFRACTION99.64
3.41-3.480.3481400.2452647X-RAY DIFFRACTION99.61
3.48-3.560.29961370.25372680X-RAY DIFFRACTION99.65
3.56-3.650.31421470.24752676X-RAY DIFFRACTION99.72
3.65-3.750.31181270.24392671X-RAY DIFFRACTION99.75
3.75-3.860.32961440.24612662X-RAY DIFFRACTION99.82
3.86-3.990.27781450.24362701X-RAY DIFFRACTION99.65
3.99-4.130.29981460.23452671X-RAY DIFFRACTION99.82
4.13-4.290.26781540.21812679X-RAY DIFFRACTION99.93
4.3-4.490.2371330.22032731X-RAY DIFFRACTION99.97
4.49-4.730.27051480.22522706X-RAY DIFFRACTION100
4.73-5.020.29021280.2232726X-RAY DIFFRACTION99.96
5.02-5.410.3251370.23312736X-RAY DIFFRACTION100
5.41-5.950.30271550.25412759X-RAY DIFFRACTION100
5.95-6.810.31141710.25122742X-RAY DIFFRACTION100
6.81-8.580.29781390.24772833X-RAY DIFFRACTION99.9
8.58-49.630.31721670.26512982X-RAY DIFFRACTION99.65

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