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

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Basic information

Entry
Database: PDB / ID: 7apr
TitleBacillithiol Disulfide Reductase Bdr (YpdA) from Staphylococcus aureus
ComponentsYpdA family putative bacillithiol disulfide reductase Bdr
KeywordsOXIDOREDUCTASE / disulfide reductase / FAD / flavoprotein / NADPH
Function / homologyBacillithiol biosynthesis thiol disulphide oxidoreductase, YpdA / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily / 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: 3.1 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
DepositionOct 19, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water43224
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 area15970 Å2
Surface area53110 Å2
Methodnative gel electrophoresis and DLS
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 area15960 Å2
Surface area53570 Å2
Methodnative gel electrophoresis and DLS
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 area14160.6 Å2
Surface area56161 Å2
Methodnative gel electrophoresis and DLS
Unit cell
γ
α
β
Length a, b, c (Å)180.308, 180.308, 350.459
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-IDDetails
d_11(chain "A" and (resid 1 through 27 or resid 29...
d_21(chain "B" and (resid 1 through 27 or resid 29...
d_31(chain "C" and (resid 1 through 27 or resid 29...
d_41(chain "D" and (resid 1 through 27 or resid 29...
d_51(chain "E" and (resid 1 through 27 or resid 29...
d_61(chain "F" and (resid 1 through 27 or resid 29...
d_71(chain "G" and (resid 1 through 27 or resid 29...
d_81(chain "H" and (resid 1 through 27 or resid 29...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_111METILEA1 - 27
d_121THRTHRA29 - 46
d_131GLNPHEA49 - 51
d_141SERGLUA53 - 68
d_151SERASNA70 - 75
d_161ALAHISA78 - 89
d_171LEUMETA91 - 105
d_181ASNTYRA107 - 129
d_191GLYGLUA131 - 178
d_1101ALAGLYA181 - 182
d_1111GLYILEA192 - 198
d_1121PHEMETA219 - 321
d_1131FADFADB
d_211METILEC1 - 27
d_221THRTHRC29 - 46
d_231GLNPHEC49 - 51
d_241SERGLUC53 - 68
d_251SERASNC70 - 75
d_261ALAHISC77 - 88
d_271LEUMETC90 - 104
d_281ASNTYRC106 - 128
d_291GLYGLUC130 - 177
d_2101ALAGLYC179 - 180
d_2111GLYILEC190 - 196
d_2121PHEMETC217 - 319
d_2131FADFADD
d_311METILEE1 - 27
d_321THRTHRE29 - 46
d_331GLNPHEE49 - 51
d_341SERGLUE54 - 69
d_351SERASNE71 - 76
d_361ALAHISE78 - 89
d_371LEUMETE93 - 107
d_381ASNTYRE109 - 131
d_391GLYGLUE134 - 181
d_3101ALAGLYE183 - 184
d_3111GLYILEE194 - 200
d_3121PHEMETE221 - 323
d_3131FADFADF
d_411METILEH1 - 27
d_421THRTHRH29 - 46
d_431GLNPHEH49 - 51
d_441SERGLUH54 - 69
d_451SERASNH71 - 76
d_461ALAHISH78 - 89
d_471LEUMETH91 - 105
d_481ASNTYRH107 - 129
d_491GLYGLUH131 - 178
d_4101ALAGLYH180 - 181
d_4111GLYILEH191 - 197
d_4121PHEMETH218 - 320
d_4131FADFADI
d_511METILEK1 - 27
d_521THRTHRK29 - 46
d_531GLNPHEK49 - 51
d_541SERGLUK53 - 68
d_551SERASNK70 - 75
d_561ALAHISK77 - 88
d_571LEUMETK90 - 104
d_581ASNTYRK108 - 130
d_591GLYGLUK132 - 179
d_5101ALAGLYK181 - 182
d_5111GLYILEK192 - 198
d_5121PHEMETK219 - 321
d_5131FADFADL
d_611METILEM1 - 27
d_621THRTHRM31 - 48
d_631GLNPHEM50 - 52
d_641SERGLUM55 - 70
d_651SERASNM74 - 79
d_661ALAHISM81 - 92
d_671LEUMETM94 - 108
d_681ASNTYRM110 - 132
d_691GLYGLUM134 - 181
d_6101ALAGLYM183 - 184
d_6111GLYILEM194 - 200
d_6121PHEMETM221 - 323
d_6131FADFADN
d_711METILEP1 - 27
d_721THRTHRP29 - 46
d_731GLNPHEP48 - 50
d_741SERGLUP52 - 67
d_751SERASNP69 - 74
d_761ALAHISP76 - 87
d_771LEUMETP89 - 103
d_781ASNTYRP105 - 127
d_791GLYGLUP129 - 176
d_7101ALAMETP178 - 289
d_7111FADFADQ
d_811METILER1 - 27
d_821THRTHRR29 - 46
d_831GLNPHER48 - 50
d_841SERGLUR52 - 67
d_851SERASNR69 - 74
d_861ALAHISR76 - 87
d_871LEUMETR89 - 103
d_881ASNTYRR105 - 127
d_891GLYGLUR129 - 176
d_8101ALAGLYR178 - 179
d_8111GLYILER189 - 195
d_8121PHEMETR216 - 318
d_8131FADFADS

NCS oper:
IDCodeMatrixVector
1given(-0.999995235861, -0.00201615855814, 0.00233738313585), (-0.00233713946133, 0.98918598038, -0.146647993507), (-0.00201644102162, -0.146652757646, -0.989185979804)-86.7515419821, -0.960529634323, -11.2933040111
2given(-0.97846157494, -0.00974419687982, 0.206198925782), (0.0414908738029, -0.987783898682, 0.150204783201), (0.202216353833, 0.155524982342, 0.966912884447)-86.4617206298, -152.885876181, 20.974791791
3given(0.980096073825, -0.00758171085094, -0.198378939741), (-0.00794803876359, -0.999967862168, -0.00105038567039), (-0.198364600552, 0.0026062023745, -0.980124835395)-1.3965033623, -155.911681631, -8.2408257909
4given(0.480184061114, 0.866110627916, -0.138836766251), (0.872789847587, -0.487558522397, -0.022903475439), (-0.0875279921014, -0.110177436205, -0.990050394248)46.8147310674, -71.7173439329, 45.8420662932
5given(-0.489296793015, -0.868682724083, 0.0773238205511), (-0.86808313536, 0.493633451841, 0.0525136680107), (-0.0837873406273, -0.0414287352348, -0.995622087666)-130.176522147, -70.9919205174, 51.7209909905
6given(-0.994913412232, 0.0601683617597, 0.0807902865641), (-0.0472824853751, -0.987113386902, 0.152877493358), (0.0889475617244, 0.148279903027, 0.984937257708)-118.844271646, -233.53137437, 22.6884893267
7given(0.995001679134, 0.0505512435259, -0.0861175376901), (0.0458452537123, -0.997390270288, -0.0557750970177), (-0.0887122947052, 0.051548234822, -0.994722528274)-33.7956216183, -229.79330783, 8.7849253014

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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 BL21(DE3) (bacteria) / References: UniProt: A0A0H2WWS2
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / 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 / Nicotinamide adenine dinucleotide phosphate


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


Mass: 18.015 Da / Num. of mol.: 24 / 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: 55.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.1 M bicine/Trizma, pH = 8.5, 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: 0.946444 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.946444 Å / Relative weight: 1
ReflectionResolution: 3.1→29.94 Å / Num. obs: 61638 / % possible obs: 99.9 % / Redundancy: 9.8 % / Biso Wilson estimate: 63.11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.125 / Rrim(I) all: 0.119 / Net I/σ(I): 14.3
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 4471 / CC1/2: 0.938 / Rrim(I) all: 0.48 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7A76
Resolution: 3.1→29.94 Å / SU ML: 0.4474 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.7985
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2908 3106 5.05 %
Rwork0.2441 58442 -
obs0.2464 61548 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.73 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20137 0 568 24 20729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002521459
X-RAY DIFFRACTIONf_angle_d0.6529231
X-RAY DIFFRACTIONf_chiral_restr0.053219
X-RAY DIFFRACTIONf_plane_restr0.00363691
X-RAY DIFFRACTIONf_dihedral_angle_d20.07227768
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
1d_2AX-RAY DIFFRACTIONTorsion NCS0.806060144939
1d_3AX-RAY DIFFRACTIONTorsion NCS1.42438564854
1d_4AX-RAY DIFFRACTIONTorsion NCS1.50118797495
1d_5AX-RAY DIFFRACTIONTorsion NCS0.815940035973
1d_6AX-RAY DIFFRACTIONTorsion NCS1.45850465346
1d_7AX-RAY DIFFRACTIONTorsion NCS2.61559634985
1d_8AX-RAY DIFFRACTIONTorsion NCS2.79362244778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.150.36371220.28892607X-RAY DIFFRACTION99.96
3.15-3.20.4051340.28922605X-RAY DIFFRACTION99.89
3.2-3.260.35371420.28462615X-RAY DIFFRACTION100
3.26-3.310.35851430.28382606X-RAY DIFFRACTION99.96
3.31-3.380.34871340.27682619X-RAY DIFFRACTION99.96
3.38-3.450.35781420.27412607X-RAY DIFFRACTION100
3.45-3.520.28921400.25392618X-RAY DIFFRACTION100
3.52-3.60.30321610.26482602X-RAY DIFFRACTION100
3.6-3.690.31831530.24282622X-RAY DIFFRACTION100
3.69-3.790.31831560.24412594X-RAY DIFFRACTION100
3.79-3.90.2661450.24952636X-RAY DIFFRACTION100
3.9-4.030.29351510.24212615X-RAY DIFFRACTION100
4.03-4.170.26231460.22442642X-RAY DIFFRACTION100
4.17-4.340.23821410.21912643X-RAY DIFFRACTION100
4.34-4.540.25941390.2162650X-RAY DIFFRACTION99.96
4.54-4.780.2541290.21392677X-RAY DIFFRACTION100
4.78-5.070.25651230.2232677X-RAY DIFFRACTION100
5.07-5.460.27221550.23222694X-RAY DIFFRACTION100
5.46-6.010.30581350.2472698X-RAY DIFFRACTION100
6.01-6.870.29751250.24672726X-RAY DIFFRACTION100
6.87-8.620.2721400.2382776X-RAY DIFFRACTION99.9
8.62-29.940.28011500.25182913X-RAY DIFFRACTION99.35

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