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- PDB-4uth: XenA - oxidized - Y183F variant -

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Basic information

Entry
Database: PDB / ID: 4uth
TitleXenA - oxidized - Y183F variant
ComponentsNADH:flavin oxidoreductase
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
FLAVIN MONONUCLEOTIDE / NADH:flavin oxidoreductase / Xenobiotic reductase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsWerther, T. / Dobbek, H.
Citation
Journal: 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.
#1: Journal: J.Mol.Biol. / Year: 2010
Title: Determinants of Substrate Binding and Protonation in the Flavoenzyme Xenobiotic Reductase A.
Authors: Spiegelhauer, O. / Werther, T. / Mende, S. / Knauer, S.H. / Dobbek, H.
History
DepositionJul 21, 2014Deposition site: PDBE / Processing site: PDBE
SupersessionAug 5, 2015ID: 3N16
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 2.0Aug 23, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_name_com / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_ref / struct_ref_seq / struct_ref_seq_dif
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 / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_gene_src_variant / _entity_src_gen.pdbx_seq_type / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 2.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

Downloads & links

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Assembly

Deposited unit
A: NADH:flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7424
Polymers40,0931
Non-polymers6483
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-31 kcal/mol
Surface area13510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.477, 83.218, 156.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein NADH:flavin oxidoreductase


Mass: 40093.223 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: B7H19_27640 / Variant: 86 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: A0A1X0ZT96, UniProt: Q3ZDM6*PLUS
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.33 Å3/Da / Density % sol: 47.18 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.25→29.24 Å / Num. obs: 103079 / % possible obs: 99.6 % / Observed criterion σ(I): 1.96 / Redundancy: 3.6 % / Biso Wilson estimate: 9.45 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.01

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→29.241 Å / SU ML: 0.1 / σ(F): 1.99 / Phase error: 16.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1642 5153 5 %
Rwork0.1358 --
obs0.1372 103065 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→29.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2777 0 41 395 3213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093063
X-RAY DIFFRACTIONf_angle_d1.2664208
X-RAY DIFFRACTIONf_dihedral_angle_d12.5631119
X-RAY DIFFRACTIONf_chiral_restr0.047442
X-RAY DIFFRACTIONf_plane_restr0.007557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2499-1.26410.29551590.24943033X-RAY DIFFRACTION95
1.2641-1.2790.2591730.23953277X-RAY DIFFRACTION100
1.279-1.29460.25441690.22163214X-RAY DIFFRACTION100
1.2946-1.3110.25111720.22353263X-RAY DIFFRACTION100
1.311-1.32820.24241700.21063245X-RAY DIFFRACTION100
1.3282-1.34640.24951690.19823207X-RAY DIFFRACTION100
1.3464-1.36570.22591720.19253268X-RAY DIFFRACTION100
1.3657-1.38610.23571710.18493243X-RAY DIFFRACTION100
1.3861-1.40770.20921710.17543251X-RAY DIFFRACTION100
1.4077-1.43080.18541710.16613239X-RAY DIFFRACTION100
1.4308-1.45550.19851710.14843250X-RAY DIFFRACTION100
1.4555-1.48190.16791700.14543232X-RAY DIFFRACTION100
1.4819-1.51040.18261720.13883275X-RAY DIFFRACTION100
1.5104-1.54130.17551700.13543220X-RAY DIFFRACTION100
1.5413-1.57480.18081720.13533282X-RAY DIFFRACTION100
1.5748-1.61140.16871720.12743253X-RAY DIFFRACTION100
1.6114-1.65170.16041700.12243238X-RAY DIFFRACTION100
1.6517-1.69640.15871730.1153286X-RAY DIFFRACTION100
1.6964-1.74630.1481710.11233256X-RAY DIFFRACTION100
1.7463-1.80260.13671720.11443265X-RAY DIFFRACTION100
1.8026-1.8670.15991720.1143272X-RAY DIFFRACTION100
1.867-1.94180.1431720.11283264X-RAY DIFFRACTION100
1.9418-2.03010.14321740.11333296X-RAY DIFFRACTION100
2.0301-2.13710.15121720.11183275X-RAY DIFFRACTION100
2.1371-2.2710.14181730.10833284X-RAY DIFFRACTION100
2.271-2.44630.14661740.11573305X-RAY DIFFRACTION100
2.4463-2.69230.1251730.11753286X-RAY DIFFRACTION100
2.6923-3.08150.14771760.12373342X-RAY DIFFRACTION100
3.0815-3.88090.13551770.1243363X-RAY DIFFRACTION100
3.8809-29.24880.16721800.14783428X-RAY DIFFRACTION98

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