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- PDB-5lni: XenA - oxidized - Y183F variant in complex with 7-hydroxycoumarin -

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Basic information

Entry
Database: PDB / ID: 5lni
TitleXenA - oxidized - Y183F variant in complex with 7-hydroxycoumarin
ComponentsNADH:flavin oxidoreductase
KeywordsOXIDOREDUCTASE / flavin mononucleotide / complex
Function / homology
Function and homology information


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
7-hydroxy-2H-chromen-2-one / FLAVIN MONONUCLEOTIDE / NADH:flavin oxidoreductase / :
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.133 Å
AuthorsWerther, T. / Dobbek, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: Nat Commun / Year: 2017
Title: Redox-dependent substrate-cofactor interactions in the Michaelis-complex of a flavin-dependent oxidoreductase
Authors: Werther, T. / Wahlefeld, S. / Salewski, J. / Kuhlmann, U. / Zebger, I. / Hildebrandt, P. / Dobbek, H.
History
DepositionAug 4, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADH:flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5469
Polymers39,2891
Non-polymers1,2578
Water8,485471
1
A: NADH:flavin oxidoreductase
hetero molecules

A: NADH:flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,09218
Polymers78,5792
Non-polymers2,51416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6570 Å2
ΔGint-117 kcal/mol
Surface area24200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.760, 83.410, 156.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-811-

HOH

21A-846-

HOH

31A-863-

HOH

41A-965-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NADH:flavin oxidoreductase / xenobiotic reductase A


Mass: 39289.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: O999_23785 / Production host: Escherichia coli (E. coli) / References: UniProt: U2SJJ2, UniProt: A0A1X0ZT96*PLUS

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Non-polymers , 5 types, 479 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-07L / 7-hydroxy-2H-chromen-2-one / 7-hydroxycoumarin


Mass: 162.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H6O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.4 M ammonium sulfate, 0.1 M HEPES/NaOH pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.13→35 Å / Num. obs: 135813 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 13.64
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.13-1.160.4233.08190.4
1.16-1.190.3543.71195.2
1.19-1.230.3094.18195.9
1.23-1.270.2754.64196.2
1.27-1.310.235.52196.6
1.31-1.350.1996.34196.9
1.35-1.410.1667.39197
1.41-1.460.1319.02197.3
1.46-1.530.10710.62197.8
1.53-1.60.08812.83197.7
1.6-1.690.07115.22198
1.69-1.790.06117.4198
1.79-1.920.05119.96198.2
1.92-2.070.04323.28198.4
2.07-2.270.04626.87197.8
2.27-2.530.07530.62199.2
2.53-2.930.0633.77199.5
2.93-3.580.04939.16199.3
3.58-5.070.04344.07199.3
5.070.04243.32198.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L5L

3l5l


Resolution: 1.133→29.372 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 12.82
RfactorNum. reflection% reflection
Rfree0.1405 2000 1.47 %
Rwork0.1182 --
obs0.1185 135806 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.25 Å2 / Biso mean: 13.4 Å2 / Biso min: 2.16 Å2
Refinement stepCycle: final / Resolution: 1.133→29.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2777 0 119 471 3367
Biso mean--16.37 25.38 -
Num. residues----359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013257
X-RAY DIFFRACTIONf_angle_d1.3954507
X-RAY DIFFRACTIONf_chiral_restr0.077466
X-RAY DIFFRACTIONf_plane_restr0.009601
X-RAY DIFFRACTIONf_dihedral_angle_d12.591214
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1331-1.16140.18151310.16868822895390
1.1614-1.19280.16651400.159317945795
1.1928-1.22790.1981410.13999387952896
1.2279-1.26760.19031390.13499392953196
1.2676-1.31290.15081420.12099453959597
1.3129-1.36540.15511420.11019493963597
1.3654-1.42760.14951430.10169526966997
1.4276-1.50280.12911430.09289608975198
1.5028-1.5970.11911430.08849606974998
1.597-1.72030.1121450.08679672981798
1.7203-1.89340.12151450.09479688983398
1.8934-2.16730.12631460.09989762990898
2.1673-2.73020.1131470.115898761002399
2.7302-29.38180.15711530.141102041035799

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