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

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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
ComponentsGlyoxalaseGlyoxalase system
KeywordsBIOSYNTHETIC PROTEIN/ANTIBIOTIC / CYANA 3.98.13 / enzyme / catalysis / chiral spiroketal / BIOSYNTHETIC PROTEIN-ANTIBIOTIC complex
Function / homologyGlyoxalase/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 / : / Glyoxalase
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
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: To Be Published
Title: The solution structure of abxF, an enzyme catalyzing the formation of chiral spiroketal of an antibiotics, (-)-ABX.
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

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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
Water0
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 / Glyoxalase system


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

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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
NameVersionDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr AnalysisVersion 2.4.2CCPNchemical shift assignment
CcpNmr AnalysisVersion 2.4.2CCPNpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
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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