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- PDB-8e5h: Old Yellow Enzyme 5 (PcOYE5) from Pseudomonas chloritidismutans -

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Basic information

Entry
Database: PDB / ID: 8e5h
TitleOld Yellow Enzyme 5 (PcOYE5) from Pseudomonas chloritidismutans
ComponentsNADH:flavin oxidoreductase
KeywordsOXIDOREDUCTASE / Old Yellow Enzyme / Ene Reductase / TIM Barrel / Flavoprotein
Function / homology: / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / FMN binding / Aldolase-type TIM barrel / oxidoreductase activity / Chem-FNR / NADH:flavin oxidoreductase
Function and homology information
Biological speciesStutzerimonas chloritidismutans AW-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 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 5 (PcOYE5) from Pseudomonas chloritidismutans
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

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Assembly

Deposited unit
A: NADH:flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0833
Polymers39,5891
Non-polymers4942
Water8,341463
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.417, 70.090, 97.877
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NADH:flavin oxidoreductase


Mass: 39589.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stutzerimonas chloritidismutans AW-1 (bacteria)
Gene: F753_20065 / Production host: Escherichia coli (E. coli) / References: UniProt: V4RWU7
#2: Chemical ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23N4O9P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG 3350, 0.1M Bis-Tris pH 5.5

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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: Mar 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.27→48.94 Å / Num. obs: 92385 / % possible obs: 99.7 % / Redundancy: 13.4 % / Biso Wilson estimate: 12.44 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.029 / Rrim(I) all: 0.106 / Net I/σ(I): 12.7 / Num. measured all: 1233665 / Scaling rejects: 1402
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
1.27-1.2912.11.1275185942900.7920.3291.1762.494.8
6.94-48.9411.90.06279316670.9890.020.06626.499.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.27→48.94 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 13.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1563 4631 5.02 %
Rwork0.1356 87652 -
obs0.1366 92283 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.91 Å2 / Biso mean: 19.1004 Å2 / Biso min: 6.8 Å2
Refinement stepCycle: final / Resolution: 1.27→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2763 0 32 463 3258
Biso mean--17.3 29.41 -
Num. residues----368
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.27-1.280.30151610.26512632279392
1.28-1.30.22051650.216129043069100
1.3-1.310.25791410.198628683009100
1.31-1.330.18561300.170429483078100
1.33-1.350.17631440.158828743018100
1.35-1.370.17991630.155129343097100
1.37-1.390.17941540.138628392993100
1.39-1.410.15841470.13829323079100
1.41-1.430.16621630.135728823045100
1.43-1.450.15151630.132328973060100
1.45-1.480.18731560.134428893045100
1.48-1.50.16361390.129429153054100
1.5-1.530.16561500.125629213071100
1.53-1.560.15761320.115229343066100
1.56-1.60.14081720.109228983070100
1.6-1.630.12941600.113329093069100
1.63-1.680.1441580.107129093067100
1.68-1.720.15241470.115629343081100
1.72-1.770.14451560.113228943050100
1.77-1.830.14331250.122429523077100
1.83-1.890.14421640.126929413105100
1.89-1.970.16531420.13829213063100
1.97-2.060.15351510.132629563107100
2.06-2.170.14791580.130129333091100
2.17-2.30.14241590.125929503109100
2.3-2.480.15651690.125629423111100
2.48-2.730.15011800.134729503130100
2.73-3.130.14281470.140730103157100
3.13-3.940.14221610.138730323193100
3.94-48.940.17021740.146831523326100

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