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- PDB-8pun: Old Yellow Enzyme from the thermophilic Ferrovum sp. JA12 -

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Basic information

Entry
Database: PDB / ID: 8pun
TitleOld Yellow Enzyme from the thermophilic Ferrovum sp. JA12
ComponentsNADPH dehydrogenase
KeywordsOXIDOREDUCTASE / OYE / thermophilic / ene-reductase / FMN / flavoenzyme
Function / homology
Function and homology information


: / NADPH dehydrogenase / NADPH dehydrogenase activity / FMN binding / NADP binding
Similarity search - Function
NADPH dehydrogenase YqjM-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-ethyl-2-(hydroxymethyl)propane-1,3-diol / FLAVIN MONONUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / YTTRIUM (III) ION / NADPH dehydrogenase
Similarity search - Component
Biological speciesFerrovum sp. JA12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPolidori, N. / Gruber, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundDOC 46-821 Austria
CitationJournal: Proteins / Year: 2025
Title: Structure, Oligomerization, and Thermal Stability of a Recently Discovered Old Yellow Enzyme.
Authors: Polidori, N. / Babin, P. / Daniel, B. / Gruber, K.
History
DepositionJul 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Feb 19, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 1.3May 14, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH dehydrogenase
B: NADPH dehydrogenase
C: NADPH dehydrogenase
D: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,82931
Polymers163,0254
Non-polymers3,80427
Water11,566642
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17400 Å2
ΔGint-115 kcal/mol
Surface area45550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.712, 187.712, 129.317
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

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
11GLYGLYSERSER(chain 'A' and (resid -1 through 12 or resid 14...AA-1 - 1218 - 31
12SERSERASNASN(chain 'A' and (resid -1 through 12 or resid 14...AA14 - 1733 - 36
13LEULEULEULEU(chain 'A' and (resid -1 through 12 or resid 14...AA19 - 8238 - 101
14ILEILEARGARG(chain 'A' and (resid -1 through 12 or resid 14...AA85 - 90104 - 109
15PHEPHEPROPRO(chain 'A' and (resid -1 through 12 or resid 14...AA92 - 144111 - 163
16PROPROLEULEU(chain 'A' and (resid -1 through 12 or resid 14...AA146 - 152165 - 171
17THRTHRARGARG(chain 'A' and (resid -1 through 12 or resid 14...AA154 - 195173 - 214
18ASPASPLYSLYS(chain 'A' and (resid -1 through 12 or resid 14...AA197 - 255216 - 274
19GLYGLYARGARG(chain 'A' and (resid -1 through 12 or resid 14...AA257 - 354276 - 373
21GLYGLYSERSER(chain 'B' and (resid -1 through 12 or resid 14...BB-1 - 1218 - 31
22SERSERASNASN(chain 'B' and (resid -1 through 12 or resid 14...BB14 - 1733 - 36
23LEULEULEULEU(chain 'B' and (resid -1 through 12 or resid 14...BB19 - 8238 - 101
24ILEILEARGARG(chain 'B' and (resid -1 through 12 or resid 14...BB85 - 90104 - 109
25PHEPHEPROPRO(chain 'B' and (resid -1 through 12 or resid 14...BB92 - 144111 - 163
26PROPROLEULEU(chain 'B' and (resid -1 through 12 or resid 14...BB146 - 152165 - 171
27THRTHRARGARG(chain 'B' and (resid -1 through 12 or resid 14...BB154 - 195173 - 214
28ASPASPLYSLYS(chain 'B' and (resid -1 through 12 or resid 14...BB197 - 255216 - 274
29GLYGLYARGARG(chain 'B' and (resid -1 through 12 or resid 14...BB257 - 354276 - 373
31GLYGLYSERSER(chain 'C' and (resid -1 through 12 or resid 14...CC-1 - 1218 - 31
32SERSERASNASN(chain 'C' and (resid -1 through 12 or resid 14...CC14 - 1733 - 36
33LEULEULEULEU(chain 'C' and (resid -1 through 12 or resid 14...CC19 - 8238 - 101
34ILEILEARGARG(chain 'C' and (resid -1 through 12 or resid 14...CC85 - 90104 - 109
35PHEPHEPROPRO(chain 'C' and (resid -1 through 12 or resid 14...CC92 - 144111 - 163
36PROPROLEULEU(chain 'C' and (resid -1 through 12 or resid 14...CC146 - 152165 - 171
37THRTHRARGARG(chain 'C' and (resid -1 through 12 or resid 14...CC154 - 195173 - 214
38ASPASPLYSLYS(chain 'C' and (resid -1 through 12 or resid 14...CC197 - 255216 - 274
39GLYGLYARGARG(chain 'C' and (resid -1 through 12 or resid 14...CC257 - 354276 - 373
41GLYGLYSERSER(chain 'D' and (resid -1 through 12 or resid 14...DD-1 - 1218 - 31
42SERSERASNASN(chain 'D' and (resid -1 through 12 or resid 14...DD14 - 1733 - 36
43LEULEULEULEU(chain 'D' and (resid -1 through 12 or resid 14...DD19 - 8238 - 101
44ILEILEARGARG(chain 'D' and (resid -1 through 12 or resid 14...DD85 - 90104 - 109
45PHEPHEPROPRO(chain 'D' and (resid -1 through 12 or resid 14...DD92 - 144111 - 163
46PROPROLEULEU(chain 'D' and (resid -1 through 12 or resid 14...DD146 - 152165 - 171
47THRTHRARGARG(chain 'D' and (resid -1 through 12 or resid 14...DD154 - 195173 - 214
48ASPASPLYSLYS(chain 'D' and (resid -1 through 12 or resid 14...DD197 - 255216 - 274
49GLYGLYARGARG(chain 'D' and (resid -1 through 12 or resid 14...DD257 - 354276 - 373

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
NADPH dehydrogenase


Mass: 40756.234 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ferrovum sp. JA12 (bacteria) / Gene: namA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0R0LNE8

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Non-polymers , 9 types, 669 molecules

#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-9D2 / 2-ethyl-2-(hydroxymethyl)propane-1,3-diol


Mass: 134.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O3
#5: Chemical
ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Y
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Cl
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 642 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 3.62 Å3/Da / Density % sol: 66.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Lanthanides mix (0.0005M Yttrium(III) chloride hexahydrate, 0.0005M Erbium(III) chloride hexahydrate, 0.0005M Terbium(III) chloride hexahydrate, 0.0005M Ytterbium(III) chloride hexahydrate), ...Details: Lanthanides mix (0.0005M Yttrium(III) chloride hexahydrate, 0.0005M Erbium(III) chloride hexahydrate, 0.0005M Terbium(III) chloride hexahydrate, 0.0005M Ytterbium(III) chloride hexahydrate), MOPSO, Bis-Tris, PEG 20000, Trimethylolpropane, NDSB 195

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.3→48.3 Å / Num. obs: 102408 / % possible obs: 99.43 % / Redundancy: 12.9 % / Biso Wilson estimate: 35.09 Å2 / CC1/2: 0.998 / Net I/σ(I): 17.09
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 10081 / CC1/2: 0.977

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.3 Å / SU ML: 0.2424 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.7269
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.205 5135 5.04 %
Rwork0.1798 96727 -
obs0.1811 101862 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.66 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10940 0 214 642 11796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002611567
X-RAY DIFFRACTIONf_angle_d0.577715722
X-RAY DIFFRACTIONf_chiral_restr0.04571672
X-RAY DIFFRACTIONf_plane_restr0.0042053
X-RAY DIFFRACTIONf_dihedral_angle_d21.78924200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.311780.25963175X-RAY DIFFRACTION99.67
2.33-2.350.24191520.26253201X-RAY DIFFRACTION99.7
2.35-2.380.271480.24793208X-RAY DIFFRACTION99.97
2.38-2.410.28921680.24193215X-RAY DIFFRACTION99.76
2.41-2.440.29941840.24393179X-RAY DIFFRACTION99.7
2.44-2.480.28271590.22273209X-RAY DIFFRACTION99.56
2.48-2.510.26881910.2323140X-RAY DIFFRACTION99.43
2.51-2.550.24351650.22553216X-RAY DIFFRACTION99.76
2.55-2.590.26891580.22253235X-RAY DIFFRACTION99.82
2.59-2.630.29491650.22033187X-RAY DIFFRACTION99.79
2.63-2.680.25971730.22873187X-RAY DIFFRACTION99.61
2.68-2.730.25171660.2043202X-RAY DIFFRACTION99.53
2.73-2.780.23781660.19863193X-RAY DIFFRACTION99.56
2.78-2.840.2281530.19473222X-RAY DIFFRACTION99.38
2.84-2.90.2511830.20043207X-RAY DIFFRACTION99.71
2.9-2.970.25641980.21133164X-RAY DIFFRACTION99.64
2.97-3.040.24991600.20443249X-RAY DIFFRACTION99.85
3.04-3.120.22611750.20523202X-RAY DIFFRACTION99.68
3.12-3.210.22421850.18473198X-RAY DIFFRACTION99.56
3.21-3.320.19921490.18373247X-RAY DIFFRACTION99.5
3.32-3.440.20791500.16933222X-RAY DIFFRACTION99.03
3.44-3.570.19161550.16513236X-RAY DIFFRACTION99.3
3.57-3.740.22331770.16223183X-RAY DIFFRACTION98.07
3.74-3.930.17961710.15773184X-RAY DIFFRACTION97.67
3.93-4.180.13531670.14493254X-RAY DIFFRACTION99.3
4.18-4.50.14891870.13693242X-RAY DIFFRACTION99.62
4.5-4.950.15781850.13883276X-RAY DIFFRACTION99.6
4.95-5.670.16941880.1583296X-RAY DIFFRACTION99.74
5.67-7.140.18251720.17883355X-RAY DIFFRACTION99.86
7.14-48.30.17422070.15833443X-RAY DIFFRACTION98.28

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