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- PDB-8epy: The solution structure of abxF in complex with its product (-)-AB... -

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Basic information

Entry
Database: PDB / ID: 8epy
TitleThe solution structure of abxF in complex with its product (-)-ABX, an enzyme catalyzing the formation of the chiral spiroketal of an anthrabenzoxocinone antibiotic, (-)-ABX
ComponentsGlyoxalase
KeywordsBIOSYNTHETIC PROTEIN/ANTIBIOTIC / CYANA 3.98.13 / enzyme / catalysis / chiral spiroketal / BIOSYNTHETIC PROTEIN-ANTIBIOTIC complex
Function / homology: / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / metal ion binding / : / Glyoxalase
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodSOLUTION NMR / na
AuthorsJia, X. / Yan, X. / Qu, X. / Mobli, M.
Funding support Australia, China, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP220103028 Australia
National Science Foundation (NSF, China)1800048 China
CitationJournal: Nat.Chem. / Year: 2025
Title: An enzymatic dual-oxa Diels–Alder reaction constructs the oxygen-bridged tricyclic acetal unit of (–)-anthrabenzoxocinone
Authors: Jia, X. / Yan, X. / Mobli, M. / Qu, X.
History
DepositionOct 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI
Revision 2.0Feb 12, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / pdbx_contact_author ...atom_site / pdbx_contact_author / pdbx_entry_details / pdbx_nmr_refine / pdbx_nmr_software / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_validate_torsion / struct_conf / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _pdbx_entry_details.has_protein_modification / _pdbx_nmr_refine.method ..._pdbx_entry_details.has_protein_modification / _pdbx_nmr_refine.method / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.name / _pdbx_nmr_software.version / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_seq_num / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num
Description: Atomic clashes
Details: The NMR complex structure has been refined within implicit water.
Provider: author / Type: Coordinate replacement
Revision 2.1Apr 23, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyoxalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6522
Polymers25,1921
Non-polymers4601
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1target function

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Components

#1: Protein Glyoxalase


Mass: 25191.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: abxF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2I6B3F9
#2: Chemical ChemComp-WOZ / (6R,16R)-3,11,13,15-tetrahydroxy-1,6,9,9-tetramethyl-6,7,9,16-tetrahydro-14H-6,16-epoxyanthra[2,3-e]benzo[b]oxocin-14-one


Mass: 460.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H24O7 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic22D 1H-15N HSQC
131isotropic12D 1H-13C HSQC
141isotropic22D 1H-13C HSQC aromatic
151isotropic22D 1H-1H NOESY - filtered
1201isotropic12D 1H-13C HSQC constant time
161isotropic13D 1H-13C NOESY aliphatic
171isotropic23D 1H-13C NOESY aliphatic - filtered
181isotropic23D 1H-13C NOESY aromatic
191isotropic23D 1H-13C NOESY aromatic - filtered
1101isotropic13D 1H-15N NOESY
1111isotropic23D 1H-15N NOESY - filtered
1121isotropic13D HNCA
1131isotropic13D (H)CCH-TOCSY
1141isotropic13D CBCA(CO)NH
1151isotropic13D (H)CCH-TOCSY
1161isotropic13D HN(CA)CB
1171isotropic13D HN(CA)CO
1181isotropic13D HNCO
1191isotropic13D HN(CA)CO

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Sample preparation

DetailsType: solution
Contents: 1.25 mM [U-100% 13C; U-100% 15N] abxF, 1.25 mM (-)-ABX, 5 % v/v [U-100% 2H] D2O, 95 % v/v H2O, 50 mM sodium chloride, 20 mM sodium phosphate, 3 mM sodium azide, 5 mM DTT, 95% H2O/5% D2O
Details: 1.25 mM 13C, 15N-abxF in 20 mM NaPO4 pH 6.6, 50 mM NaCl, 5 mM DTT, 3 mM NaN3, pH 6.6. abxF protein sample was mixed with (-)-ABX in DMSO at the ratio of [abxF]:[(-)-ABX] = 1:2. Then excess (- ...Details: 1.25 mM 13C, 15N-abxF in 20 mM NaPO4 pH 6.6, 50 mM NaCl, 5 mM DTT, 3 mM NaN3, pH 6.6. abxF protein sample was mixed with (-)-ABX in DMSO at the ratio of [abxF]:[(-)-ABX] = 1:2. Then excess (-)-ABX and DMSO was removed by buffer exchange using Amicon.
Label: 13C, 15N_abxF with (-)-ABX / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.25 mMabxF[U-100% 13C; U-100% 15N]1
1.25 mM(-)-ABXnatural abundance1
5 % v/vD2O[U-100% 2H]1
95 % v/vH2Onatural abundance1
50 mMsodium chloridenatural abundance1
20 mMsodium phosphatenatural abundance1
3 mMsodium azidenatural abundance1
5 mMDTTnatural abundance1
Sample conditionsDetails: 1.25 mM 13C, 15N-abxF and 1.25 mM (-)-ABX in 20 mM NaPO4 pH 6.6, 50 mM NaCl, 5 mM DTT, 3 mM NaN3, pH 6.6.
Ionic strength: 20 mM sodium phosphate and 50 mM NaCl mM / Label: condtions_1 / pH: 6.6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisVranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, and Laue ED. CcpNmr Analysis Version 2chemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
XTBChristoph Bannwarth, Eike Caldeweyher, Sebastian Ehlert, Andreas Hansen, Philipp Pracht, Jakob Seibert, Sebastian Spicher, Stefan Grimmerefinement
CcpNmr AnalysisVranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, and Laue ED. CcpNmr Analysis Version 2peak picking
RefinementMethod: na / Software ordinal: 3
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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