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- PDB-8j59: The structure of a novel thermophilic-like old yellow enzyme from... -

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Basic information

Entry
Database: PDB / ID: 8j59
TitleThe structure of a novel thermophilic-like old yellow enzyme from Aspergillus flavus-AfOYE1
ComponentsNADPH dehydrogenase afvA
KeywordsBIOSYNTHETIC PROTEIN / Thermophilic-like / old yellow enzyme / alkenes / enantioselectivity
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-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NITRATE ION / NADPH dehydrogenase afvA
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLi, N. / Wang, Y.
Funding support China, 4items
OrganizationGrant numberCountry
Other government232102311151
Other government22A180013
National Natural Science Foundation of China (NSFC)31900876 China
Other government2019BS020
CitationJournal: To Be Published
Title: The structure of a novel thermophilic-like old yellow enzyme from Aspergillus flavus-AfOYE1
Authors: Li, N. / Wang, Y.
History
DepositionApr 21, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH dehydrogenase afvA
B: NADPH dehydrogenase afvA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,30917
Polymers84,5822
Non-polymers1,72615
Water16,574920
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-31 kcal/mol
Surface area28020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.473, 171.422, 50.478
Angle α, β, γ (deg.)90.000, 117.600, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NADPH dehydrogenase afvA / Aflavarin synthesis protein A


Mass: 42291.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / IAM 13836 / NRRL 3357 / JCM 12722 / SRRC 167) (mold)
Gene: afvA, AFLA_108540 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8N8Q9, NADPH dehydrogenase

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Non-polymers , 6 types, 935 molecules

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


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 920 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris propane, pH 6.5, 15% (W/v) PEG3350, 0.2 M sodium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.55→42.86 Å / Num. obs: 102393 / % possible obs: 99.28 % / Redundancy: 6.5 % / Biso Wilson estimate: 9.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.02 / Rrim(I) all: 0.05 / Net I/σ(I): 25.71
Reflection shellResolution: 1.55→1.605 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 7.66 / Num. unique obs: 9786 / CC1/2: 0.98 / Rpim(I) all: 0.08 / Rrim(I) all: 0.19 / % possible all: 95.09

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487_1692refinement
XDSversion 1.12 (25-MAR-2022)data scaling
Cootcoot 0.8.9.2 EL (CCP4)model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→42.86 Å / SU ML: 0.1402 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.5661
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1674 4940 4.83 %
Rwork0.1439 97416 -
obs0.1451 102356 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.12 Å2
Refinement stepCycle: LAST / Resolution: 1.55→42.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5932 0 112 920 6964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00636205
X-RAY DIFFRACTIONf_angle_d0.92368427
X-RAY DIFFRACTIONf_chiral_restr0.0574935
X-RAY DIFFRACTIONf_plane_restr0.00851086
X-RAY DIFFRACTIONf_dihedral_angle_d13.3676896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.22481600.16792913X-RAY DIFFRACTION88.89
1.57-1.590.21021640.16263172X-RAY DIFFRACTION96.5
1.59-1.610.15861430.15593234X-RAY DIFFRACTION100
1.61-1.630.17551700.1563319X-RAY DIFFRACTION99.97
1.63-1.650.21281540.14423243X-RAY DIFFRACTION99.97
1.65-1.670.19761610.14343225X-RAY DIFFRACTION100
1.67-1.690.17331340.13933374X-RAY DIFFRACTION100
1.69-1.720.16761520.14723203X-RAY DIFFRACTION99.91
1.72-1.750.17492130.14343279X-RAY DIFFRACTION99.97
1.75-1.770.16051810.14333181X-RAY DIFFRACTION99.97
1.77-1.80.16641520.14323320X-RAY DIFFRACTION99.97
1.8-1.840.19051400.1433271X-RAY DIFFRACTION99.82
1.84-1.870.1811560.15023302X-RAY DIFFRACTION99.88
1.87-1.910.17621400.15983238X-RAY DIFFRACTION99.38
1.91-1.950.19581790.17033251X-RAY DIFFRACTION98.88
1.95-20.17881840.14973194X-RAY DIFFRACTION99.97
2-2.050.1771630.1443294X-RAY DIFFRACTION100
2.05-2.10.15471730.14983250X-RAY DIFFRACTION99.07
2.1-2.170.16411470.1373246X-RAY DIFFRACTION99.85
2.17-2.240.1591600.14233263X-RAY DIFFRACTION99.8
2.24-2.320.16681460.14383265X-RAY DIFFRACTION99.1
2.32-2.410.14831410.14633316X-RAY DIFFRACTION100
2.41-2.520.17261510.14563272X-RAY DIFFRACTION99.97
2.52-2.650.17221980.15023248X-RAY DIFFRACTION100
2.65-2.820.17642050.15133214X-RAY DIFFRACTION99.42
2.82-3.030.18811590.15033247X-RAY DIFFRACTION99.77
3.03-3.340.18521680.1473277X-RAY DIFFRACTION100
3.34-3.820.1471870.13043257X-RAY DIFFRACTION99.62
3.82-4.810.12881680.11643251X-RAY DIFFRACTION99.42
4.81-42.860.14261910.1383297X-RAY DIFFRACTION99.66
Refinement TLS params.Method: refined / Origin x: -4.13522411782 Å / Origin y: -1.48831351728 Å / Origin z: 12.1347809184 Å
111213212223313233
T0.0417697395222 Å20.0017631721455 Å2-0.00235635590059 Å2-0.0942827965242 Å2-0.00172378761517 Å2--0.0380194202267 Å2
L0.0426424207542 °2-0.000479207779055 °2-0.0160836316728 °2-0.537196487682 °2-0.00120555658937 °2--0.0352079454706 °2
S-0.00331913527402 Å °0.00754083633152 Å °0.000499503734 Å °-0.0160432708551 Å °0.00495985613556 Å °0.0218888584105 Å °-0.000318712797173 Å °-0.00202576287036 Å °-0.00177125168585 Å °
Refinement TLS groupSelection details: all

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