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- PDB-7fev: Crystal structure of Old Yellow Enzyme6 (OYE6) -

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Basic information

Entry
Database: PDB / ID: 7fev
TitleCrystal structure of Old Yellow Enzyme6 (OYE6)
ComponentsFMN binding
KeywordsOXIDOREDUCTASE / Flavoenzyme / Ascochyta rabiei / FMN-binding / Fungal OYEs
Function / homologyNADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / FMN binding / Aldolase-type TIM barrel / oxidoreductase activity / FLAVIN MONONUCLEOTIDE / FMN binding
Function and homology information
Biological speciesAscochyta rabiei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.594 Å
AuthorsSingh, Y. / Sharma, R. / Mishra, M. / Verma, P.K. / Saxena, A.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: Febs J. / Year: 2022
Title: Crystal structure of ArOYE6 reveals a novel C-terminal helical extension and mechanistic insights into the distinct class III OYEs from pathogenic fungi.
Authors: Singh, Y. / Sharma, R. / Mishra, M. / Verma, P.K. / Saxena, A.K.
History
DepositionJul 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 25, 2022Group: Structure summary / Category: audit_author
Revision 1.3Sep 28, 2022Group: 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 1.4Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FMN binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6372
Polymers49,1801
Non-polymers4561
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-6 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.850, 59.137, 122.806
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 FMN binding / Old yellow enzyme 6


Mass: 49180.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ascochyta rabiei (fungus) / Gene: ST47_g1359 / Production host: Escherichia coli (E. coli) / References: UniProt: W8PB08
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.14 Å3/Da / Density % sol: 36.96 % / Description: Plate shaped crystals were observed
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5; bicine, 0.10 M carboxylic acid;37.5% MPD, PEG1000 and PEG3350
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2016
RadiationMonochromator: Variable line spacing plane grating / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 58195 / % possible obs: 92.3 % / Redundancy: 7.4 % / Biso Wilson estimate: 21.83 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.036 / Rrim(I) all: 0.099 / Χ2: 2.379 / Net I/σ(I): 9.9 / Num. measured all: 428330
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.536.30.84430860.7640.3580.9181.11199.4
1.53-1.556.90.71230850.8460.290.7690.78499.7
1.55-1.587.30.62530920.8690.2460.6720.76599.8
1.58-1.627.50.53931170.9080.210.5790.79599.8
1.62-1.657.50.45431260.9440.1760.4870.805100
1.65-1.697.60.39531090.9550.1520.4240.82899.9
1.69-1.737.60.3431130.970.1310.3640.946100
1.73-1.787.70.26531060.9770.1020.2840.877100
1.78-1.837.70.22431310.9810.0860.240.963100
1.83-1.897.10.24925830.9790.0980.2681.25982.5
1.89-1.965.80.26322320.9490.1050.2848.10271.2
1.96-2.047.80.12431450.9940.0470.1331.426100
2.04-2.137.80.10831360.9950.0410.1161.787100
2.13-2.247.30.13821340.980.0550.1494.11568.2
2.24-2.387.20.12621640.9820.050.1354.98368.3
2.38-2.567.80.07531680.9940.0290.082.409100
2.56-2.827.80.07231930.9960.0280.0773.14100
2.82-3.237.80.06531840.9970.0250.073.896100
3.23-4.076.70.07318980.9940.0290.0787.7458.2
4.07-507.20.05833930.9930.0230.0636.72499.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KRU

3kru


Resolution: 1.594→19.703 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.199 2478 4.87 %
Rwork0.1719 48450 -
obs0.1733 50928 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.98 Å2 / Biso mean: 29.3186 Å2 / Biso min: 12.05 Å2
Refinement stepCycle: final / Resolution: 1.594→19.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3429 0 31 261 3721
Biso mean--18.03 34.2 -
Num. residues----420
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.594-1.62450.30571100.2625236387
1.6245-1.65760.3271360.2414268498
1.6576-1.69370.27911590.2405265599
1.6937-1.7330.28021530.2234268399
1.733-1.77640.24231370.2181270699
1.7764-1.82430.2671230.2009272399
1.8243-1.8780.22561290.1915271899
1.878-1.93860.20691340.1865271899
1.9386-2.00780.24581420.179271099
2.0078-2.08810.21611250.1721275599
2.0881-2.1830.18361490.1699269699
2.183-2.29790.21091530.1743271099
2.2979-2.44170.2331330.1794272399
2.4417-2.62980.21171220.1783274498
2.6298-2.89370.20291540.1792269798
2.8937-3.31070.20091470.1805272497
3.3107-4.16460.16431080.1456272996
4.1646-19.7030.15451640.1448271292
Refinement TLS params.Method: refined / Origin x: 16.0772 Å / Origin y: 0.7484 Å / Origin z: 17.9679 Å
111213212223313233
T0.1133 Å20.0055 Å2-0.0131 Å2-0.1287 Å20.0005 Å2--0.1298 Å2
L1.0816 °2-0.3458 °2-0.2847 °2-1.3011 °20.0906 °2--1.2165 °2
S-0.0114 Å °-0.0442 Å °-0.0138 Å °-0.0378 Å °-0 Å °-0.0676 Å °-0.0107 Å °0.1145 Å °0.0149 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 445
2X-RAY DIFFRACTION1allC401
3X-RAY DIFFRACTION1allS1 - 375

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