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- PDB-4utl: XenA - reduced - Y183F variant in complex with coumarin -

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Basic information

Entry
Database: PDB / ID: 4utl
TitleXenA - reduced - Y183F variant in complex with coumarin
ComponentsXENOBIOTIC REDUCTASE
KeywordsOXIDOREDUCTASE
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
COUMARIN / Chem-FNR / Xenobiotic reductase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.229 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
DepositionJul 21, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: XENOBIOTIC REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4249
Polymers40,0931
Non-polymers1,3318
Water5,819323
1
A: XENOBIOTIC REDUCTASE
hetero molecules

A: XENOBIOTIC REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,84918
Polymers80,1862
Non-polymers2,66216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.812, 83.525, 157.331
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2260-

HOH

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Components

#1: Protein XENOBIOTIC REDUCTASE / XENOBIOTIC REDUCTASE A


Mass: 40093.223 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Strain: 86 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q3ZDM6, NADPH dehydrogenase
#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-COU / COUMARIN / 2H-1-BENZOPYRAN-2-ONE / Coumarin


Mass: 146.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNO GENOMIC SEQUENCE DATA ARE AVAILABLE FOR THIS SPECIAL STRAIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.07 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Type: BESSY / Wavelength: 0.91841
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.23→36.89 Å / Num. obs: 110002 / % possible obs: 99.4 % / Observed criterion σ(I): 2.6 / Redundancy: 3.6 % / Biso Wilson estimate: 10.54 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.94

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L5L

3l5l


Resolution: 1.229→36.887 Å / SU ML: 0.1 / σ(F): 1.99 / Phase error: 13.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1417 2000 1.8 %
Rwork0.1206 --
obs0.1209 110001 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.229→36.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2777 0 90 323 3190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093156
X-RAY DIFFRACTIONf_angle_d1.3184347
X-RAY DIFFRACTIONf_dihedral_angle_d13.0181154
X-RAY DIFFRACTIONf_chiral_restr0.078452
X-RAY DIFFRACTIONf_plane_restr0.009571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2289-1.25970.23351380.19027469X-RAY DIFFRACTION98
1.2597-1.29370.23671430.17027670X-RAY DIFFRACTION100
1.2937-1.33180.19691420.15257683X-RAY DIFFRACTION100
1.3318-1.37480.18971430.13897708X-RAY DIFFRACTION100
1.3748-1.42390.1671410.12617681X-RAY DIFFRACTION100
1.4239-1.48090.14981440.10897711X-RAY DIFFRACTION100
1.4809-1.54830.13271420.0987685X-RAY DIFFRACTION100
1.5483-1.630.12691420.09487712X-RAY DIFFRACTION100
1.63-1.73210.14321440.09127748X-RAY DIFFRACTION100
1.7321-1.86580.12721430.09577733X-RAY DIFFRACTION100
1.8658-2.05360.12251430.09997713X-RAY DIFFRACTION100
2.0536-2.35070.11861440.10067773X-RAY DIFFRACTION99
2.3507-2.96140.13361430.1237756X-RAY DIFFRACTION99
2.9614-36.90330.13661480.13777959X-RAY DIFFRACTION98

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