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- PDB-8e5i: Old Yellow Enzyme 1 (NpOYE1) from Neptuniibacter sp. -

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Basic information

Entry
Database: PDB / ID: 8e5i
TitleOld Yellow Enzyme 1 (NpOYE1) from Neptuniibacter sp.
ComponentsAlkene reductase
KeywordsOXIDOREDUCTASE / Old Yellow Enzyme / Ene Reductase / TIM Barrel / Flavoprotein
Function / homologyOxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / FMN binding / Aldolase-type TIM barrel / oxidoreductase activity / FLAVIN MONONUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Alkene reductase
Function and homology information
Biological speciesNeptuniibacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFrkic, R.L. / Jackson, C.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE200100012 Australia
CitationJournal: To Be Published
Title: Old Yellow Enzyme 1 (NpOYE1) from Neptuniibacter sp.
Authors: Frkic, R.L. / Jackson, C.J.
History
DepositionAug 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkene reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0096
Polymers39,2991
Non-polymers7105
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.298, 95.298, 87.602
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-583-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alkene reductase


Mass: 39299.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neptuniibacter sp. (bacteria) / Gene: AXW15_12265 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A136H5V4

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Non-polymers , 5 types, 200 molecules

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


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% PEG 3350, Bis-tris propane pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→47.65 Å / Num. obs: 45093 / % possible obs: 100 % / Redundancy: 26.6 % / Biso Wilson estimate: 26.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.031 / Rrim(I) all: 0.16 / Net I/σ(I): 16.6 / Num. measured all: 1198035 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.7326.33.9256193323560.5170.7744.0021.499.6
8.99-47.6521.10.04980793820.9990.010.05154.799.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.8data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold

Resolution: 1.7→47.65 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1951 2235 4.96 %
Rwork0.1608 42783 -
obs0.1624 45018 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.54 Å2 / Biso mean: 33.7927 Å2 / Biso min: 16.72 Å2
Refinement stepCycle: final / Resolution: 1.7→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2742 0 47 195 2984
Biso mean--30.9 41.15 -
Num. residues----357
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.740.3231390.294526242763
1.74-1.780.29091320.254126232755
1.78-1.820.28521500.226226152765
1.82-1.870.22981370.193626542791
1.87-1.920.20961290.18226202749
1.92-1.990.22051510.181826512802
1.99-2.060.22191300.174526432773
2.06-2.140.18211480.150926282776
2.14-2.240.18271610.147226362797
2.24-2.360.17951280.149726732801
2.36-2.50.19731210.157427002821
2.5-2.70.22161280.174326782806
2.7-2.970.19071580.177526672825
2.97-3.40.19041120.169827482860
3.4-4.280.17851540.130527272881
4.28-47.650.17881570.147928963053
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)
12.04470.6466-0.05444.037-0.84161.67070.0078-0.1269-0.10580.136-0.00590.1989-0.0176-0.2063-0.01380.19740.03510.00970.2228-0.00010.18264.747-19.681.951
21.8836-0.88570.44371.9816-0.78351.4597-0.051-0.072-0.16610.07640.0121-0.02990.08450.03520.04770.1863-0.0019-0.00330.16080.00370.204816.639-31.391-0.418
31.4476-0.6966-0.27752.5181-0.30391.56540.00840.00540.11070.0585-0.0809-0.3644-0.14560.25340.05290.2369-0.0313-0.02360.26110.00950.273225.43-15.91-3.732
42.2019-0.8699-0.16993.15930.4940.8826-0.0402-0.25770.35860.38930.06940.2035-0.5253-0.1411-0.02480.43190.04780.01280.2398-0.03540.24099.854-5.0879.353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 14:86 )A14 - 86
2X-RAY DIFFRACTION2( CHAIN A AND RESID 87:230 )A87 - 230
3X-RAY DIFFRACTION3( CHAIN A AND RESID 231:325 )A231 - 325
4X-RAY DIFFRACTION4( CHAIN A AND RESID 326:360 )A326 - 360

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