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- PDB-8stb: The structure of abxF, an enzyme catalyzing the formation of the ... -

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Basic information

Entry
Database: PDB / ID: 8stb
TitleThe structure of abxF, an enzyme catalyzing the formation of the chiral spiroketal of an anthrabenzoxocinone antibiotic, (-)-ABX
ComponentsGlyoxalase
KeywordsBIOSYNTHETIC PROTEIN / Diels-Alderase / biosynthesis / antibiotics / chiral spiroketal
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsLuo, Z. / Jia, X. / Yan, X. / Qu, X. / Kobe, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FL180100109 Australia
CitationJournal: Nat.Chem. / Year: 2025
Title: An enzymatic dual-oxa Diels-Alder reaction constructs the oxygen-bridged tricyclic acetal unit of (-)-anthrabenzoxocinone.
Authors: Yan, X. / Jia, X. / Luo, Z. / Ji, S. / Zhang, M.J. / Zhang, H. / Yu, M. / Orts, J. / Jiang, K. / Lin, Z. / Deng, Z. / Kong, X.D. / Kobe, B. / Zhao, Y.L. / Mobli, M. / Qu, X.
History
DepositionMay 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 2.0Jun 4, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / citation / citation_author / entity / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_sheet_range
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _software.version / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _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_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id
Description: Ligand identity / Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Glyoxalase
A: Glyoxalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3106
Polymers47,9912
Non-polymers3194
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, gel filtration, AbxF protein was further purified by a superdex s200 column.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.029, 76.029, 166.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Glyoxalase


Mass: 23995.695 Da / Num. of mol.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2 M ammonium sulphate, 0.001 M zinc chloride, and 0.1 M Bis-tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 0.95374 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.22→45.255 Å / Num. obs: 24967 / % possible obs: 98.02 % / Redundancy: 26.5 % / Biso Wilson estimate: 40.45 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.1897 / Rpim(I) all: 0.03794 / Rrim(I) all: 0.1936 / Net I/σ(I): 13.25
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 27 % / Rmerge(I) obs: 0.4371 / Num. unique obs: 2294 / CC1/2: 0.978 / CC star: 0.994 / Rpim(I) all: 0.0845 / Rrim(I) all: 0.4453 / % possible all: 93.79

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→45.18 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 22.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2306 2380 9.72 %
Rwork0.1959 --
obs0.1994 24495 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3127 0 13 79 3219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093214
X-RAY DIFFRACTIONf_angle_d1.0614382
X-RAY DIFFRACTIONf_dihedral_angle_d15.5091114
X-RAY DIFFRACTIONf_chiral_restr0.059478
X-RAY DIFFRACTIONf_plane_restr0.009576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.270.28081300.18581212X-RAY DIFFRACTION94
2.27-2.310.23671380.1861217X-RAY DIFFRACTION95
2.31-2.370.22581460.18281231X-RAY DIFFRACTION96
2.37-2.430.23131410.18911253X-RAY DIFFRACTION96
2.43-2.490.29911300.23071262X-RAY DIFFRACTION97
2.49-2.570.30551340.22111282X-RAY DIFFRACTION98
2.57-2.650.28311210.19381294X-RAY DIFFRACTION98
2.65-2.740.22151360.18051288X-RAY DIFFRACTION99
2.74-2.850.22581320.1991290X-RAY DIFFRACTION98
2.85-2.980.25281340.2141314X-RAY DIFFRACTION99
2.98-3.140.30431350.24711309X-RAY DIFFRACTION99
3.14-3.340.22341410.20741319X-RAY DIFFRACTION99
3.34-3.60.25031230.19711347X-RAY DIFFRACTION100
3.6-3.960.24781460.18611339X-RAY DIFFRACTION100
3.96-4.530.15511510.15811337X-RAY DIFFRACTION100
4.53-5.70.19111570.17151370X-RAY DIFFRACTION100
5.71-45.180.25481850.22861451X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3273-1.2475-0.98961.0276-0.31082.21330.01850.15130.3782-0.12250.01910.2039-0.165-0.211500.33260.0465-0.02340.37960.07560.313.1997-11.135511.2161
23.26310.031-0.70832.2638-0.14680.3404-0.1281-0.04420.12790.16310.0945-0.0075-0.00250.028-0.00070.32460.0359-0.03690.40770.01840.256112.4791-15.315517.0489
31.5745-0.80890.15670.46590.2550.6892-0.1339-0.1889-0.5809-0.0470.1153-0.45180.35840.41640.00080.47880.1005-0.05390.4497-0.03360.610912.9969-28.7758-12.6488
41.25030.50330.55491.2561-0.21240.3688-0.3642-0.5811-1.23680.37790.0589-0.04890.40670.6367-0.00780.49790.1372-0.0650.6780.02450.880517.4778-30.0938-8.6189
51.0578-0.2010.58730.46030.20182.2057-0.09860.26570.2291-0.29970.0053-0.5325-0.45160.86020.0080.3219-0.054-0.0240.505-0.01770.423617.0599-10.0227-10.757
61.60340.5212-0.43730.4698-0.64261.848-0.09510.1597-0.0865-0.21180.0424-0.1106-0.18440.4488-0.00010.32750.01960.02240.4157-0.02220.379911.3445-13.9469-17.517
70.17970.11250.242-0.01620.07280.714-0.13050.13660.1398-0.5450.1379-0.14760.08960.3531-0.00030.3888-0.02110.01130.41050.00740.35544.2933-14.0305-24.3374
80.192-0.11240.02040.3748-0.34110.54140.08580.4524-0.4815-0.1037-0.06-0.13730.21080.0958-0.00240.44620.087-0.02440.4331-0.10660.60264.9559-31.3855-20.9734
90.6914-0.0881-0.21750.20020.14180.11940.16370.2827-0.4963-0.0830.0559-0.11550.38470.13760.00030.38270.0232-0.03760.377-0.0560.38361.717-28.6559-21.0057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 11 through 97 )
2X-RAY DIFFRACTION2chain 'B' and (resid 98 through 244 )
3X-RAY DIFFRACTION3chain 'A' and (resid 11 through 37 )
4X-RAY DIFFRACTION4chain 'A' and (resid 38 through 76 )
5X-RAY DIFFRACTION5chain 'A' and (resid 77 through 111 )
6X-RAY DIFFRACTION6chain 'A' and (resid 112 through 166 )
7X-RAY DIFFRACTION7chain 'A' and (resid 167 through 194 )
8X-RAY DIFFRACTION8chain 'A' and (resid 195 through 212 )
9X-RAY DIFFRACTION9chain 'A' and (resid 213 through 244 )

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