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- PDB-5lnj: XenA - reduced - Y183F variant in complex with 7-hydroxycoumarin -

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Basic information

Entry
Database: PDB / ID: 5lnj
TitleXenA - reduced - 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 / Chem-FNR / NADH:flavin oxidoreductase / :
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.16 Å
AuthorsWerther, T. / Dobbek, H.
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

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Assembly

Deposited unit
A: NADH:flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4517
Polymers39,4461
Non-polymers1,0056
Water6,918384
1
A: NADH:flavin oxidoreductase
hetero molecules

A: NADH:flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,90214
Polymers78,8932
Non-polymers2,01012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6130 Å2
ΔGint-122 kcal/mol
Surface area24460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.620, 83.460, 156.870
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-785-

HOH

21A-793-

HOH

31A-806-

HOH

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Components

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


Mass: 39446.453 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
#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-07L / 7-hydroxy-2H-chromen-2-one / 7-hydroxycoumarin


Mass: 162.142 Da / Num. of mol.: 1 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.4 M ammonium sulfate, 0.1 M HEPES/NaOH pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.16→27.043 Å / Num. obs: 129888 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 12.73
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.16-1.190.5862.36199.7
1.19-1.220.4862.87199.7
1.22-1.260.4313.22199.7
1.26-1.30.3563.95199.7
1.3-1.340.2984.67199.8
1.34-1.390.2535.39199.8
1.39-1.440.1966.78199.8
1.44-1.50.1538.41199.8
1.5-1.560.11910.34199.7
1.56-1.640.09212.8199.6
1.64-1.730.07515.28199.6
1.73-1.830.06118.05199.4
1.83-1.960.05121.34199.2
1.96-2.120.04325.27199.3
2.12-2.320.0428.54198.9
2.32-2.590.03729.61199.2
2.59-30.03431.5199.3
3-3.670.0334.02199.1
3.67-5.190.03135.44199.1
5.190.03534.23197.6

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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: 1.16→27.043 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 14.43
RfactorNum. reflection% reflection
Rfree0.1452 1999 1.54 %
Rwork0.1272 --
obs0.1274 129872 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 55.15 Å2 / Biso mean: 14.29 Å2 / Biso min: 3.15 Å2
Refinement stepCycle: final / Resolution: 1.16→27.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2788 0 89 384 3261
Biso mean--15.17 28.09 -
Num. residues----360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093281
X-RAY DIFFRACTIONf_angle_d1.3724527
X-RAY DIFFRACTIONf_chiral_restr0.078467
X-RAY DIFFRACTIONf_plane_restr0.008602
X-RAY DIFFRACTIONf_dihedral_angle_d12.2141210
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 (%)
1.16-1.1890.24221410.189890279168100
1.189-1.22120.21441420.17290749216100
1.2212-1.25710.20951420.161790759217100
1.2571-1.29770.19551420.143690919233100
1.2977-1.3440.16311420.132490799221100
1.344-1.39790.14741430.123890849227100
1.3979-1.46150.12221420.113991259267100
1.4615-1.53850.12211430.107690889231100
1.5385-1.63490.14071420.103991479289100
1.6349-1.76110.10251420.104691159257100
1.7611-1.93830.15831430.10949128927199
1.9383-2.21870.12751430.10799147929099
2.2187-2.79480.13691430.12039202934599
2.7948-27.05070.1451490.14329491964099

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