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- PDB-4utk: XenA - reduced - Y183F variant -

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Basic information

Entry
Database: PDB / ID: 4utk
TitleXenA - reduced - Y183F variant
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
Chem-FNR / Xenobiotic reductase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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 2.0Aug 16, 2017Group: Atomic model / Database references / Category: atom_site / citation / citation_author
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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 2.1Sep 13, 2017Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 2.2Jan 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)40,8405
Polymers40,0931
Non-polymers7474
Water7,314406
1
A: XENOBIOTIC REDUCTASE
hetero molecules

A: XENOBIOTIC REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,68010
Polymers80,1862
Non-polymers1,4938
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5550 Å2
ΔGint-102.7 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.670, 83.450, 157.130
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-2078-

HOH

21A-2329-

HOH

31A-2365-

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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.36 Å3/Da / Density % sol: 47.83 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.44→28.84 Å / Num. obs: 68214 / % possible obs: 99 % / Observed criterion σ(I): 2.25 / Redundancy: 3.6 % / Biso Wilson estimate: 12.71 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.63
Reflection shellResolution: 1.44→1.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.25 / % possible all: 99.54

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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: 1.44→28.835 Å / SU ML: 0.12 / σ(F): 1.99 / Phase error: 16.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1777 2000 2.9 %
Rwork0.1464 --
obs0.1473 68210 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.44→28.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2777 0 46 406 3229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113047
X-RAY DIFFRACTIONf_angle_d1.2194183
X-RAY DIFFRACTIONf_dihedral_angle_d12.7731112
X-RAY DIFFRACTIONf_chiral_restr0.071439
X-RAY DIFFRACTIONf_plane_restr0.007551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.4760.23781420.2044704X-RAY DIFFRACTION99
1.476-1.51590.2391420.1834712X-RAY DIFFRACTION100
1.5159-1.56050.20071430.17264695X-RAY DIFFRACTION100
1.5605-1.61090.18471420.15474722X-RAY DIFFRACTION100
1.6109-1.66850.22121420.14764710X-RAY DIFFRACTION100
1.6685-1.73520.18331430.14494722X-RAY DIFFRACTION100
1.7352-1.81420.20451420.14344714X-RAY DIFFRACTION99
1.8142-1.90980.18141420.13974712X-RAY DIFFRACTION99
1.9098-2.02950.17061420.1344703X-RAY DIFFRACTION99
2.0295-2.18610.15971420.13284684X-RAY DIFFRACTION98
2.1861-2.4060.16731420.13414705X-RAY DIFFRACTION98
2.406-2.75390.1711420.13864726X-RAY DIFFRACTION98
2.7539-3.46870.17091450.14474770X-RAY DIFFRACTION99
3.4687-28.84080.1661490.1514931X-RAY DIFFRACTION98

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