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- PDB-7pxo: Structure of the Diels Alderase enzyme AbyU, from Micromonospora ... -

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Entry
Database: PDB / ID: 7pxo
TitleStructure of the Diels Alderase enzyme AbyU, from Micromonospora maris, co-crystallised with a non transformable substrate analogue
ComponentsYD repeat-containing protein
KeywordsLIGASE / Diels Alderase / Complex / Abyssomicin / substrate
Function / homologyAllene oxide cyclase barrel-like domain / Allene oxide cyclase barrel like domain / antibiotic biosynthetic process / isomerase activity / Chem-8IF / YD repeat-containing protein
Function and homology information
Biological speciesMicromonospora maris AB-18-032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBack, C.R. / Race, P.R.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T001968/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M012107/1 United Kingdom
Engineering and Physical Sciences Research CouncilBB/L01386X/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/L016494/1 United Kingdom
Citation
Journal: Chem Sci / Year: 2024
Title: Delineation of the complete reaction cycle of a natural Diels-Alderase.
Authors: Maschio, L. / Back, C.R. / Alnawah, J. / Bowen, J.I. / Johns, S.T. / Mbatha, S.Z. / Han, L.C. / Lees, N.R. / Zorn, K. / Stach, J.E.M. / Hayes, M.A. / van der Kamp, M.W. / Pudney, C.R. / ...Authors: Maschio, L. / Back, C.R. / Alnawah, J. / Bowen, J.I. / Johns, S.T. / Mbatha, S.Z. / Han, L.C. / Lees, N.R. / Zorn, K. / Stach, J.E.M. / Hayes, M.A. / van der Kamp, M.W. / Pudney, C.R. / Burston, S.G. / Willis, C.L. / Race, P.R.
#1: Journal: Biorxiv / Year: 2024
Title: Delineation of the Complete Reaction Cycle of a Natural Diels-Alderase
Authors: Maschio, L. / Back, C.R. / Alnawah, J. / Bowen, J.I. / Johns, S.T. / Mbatha, S.Z. / Han, L.C. / Lees, N.R. / Zorn, K. / Stach, J.E.M. / Hayes, M.A. / van der Kamp, M.W. / Pudney, C.R. / ...Authors: Maschio, L. / Back, C.R. / Alnawah, J. / Bowen, J.I. / Johns, S.T. / Mbatha, S.Z. / Han, L.C. / Lees, N.R. / Zorn, K. / Stach, J.E.M. / Hayes, M.A. / van der Kamp, M.W. / Pudney, C.R. / Burston, S.G. / Willis, C.L. / Race, P.R.
History
DepositionOct 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Apr 24, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / database_PDB_caveat ...atom_site / database_PDB_caveat / entity_poly / entity_src_gen / pdbx_contact_author / pdbx_database_status / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _entity_poly.pdbx_strand_id / _entity_src_gen.gene_src_strain ..._entity_poly.pdbx_strand_id / _entity_src_gen.gene_src_strain / _pdbx_database_status.pdb_format_compatible / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _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_strand_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _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_asym_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_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_R_Free_selection_details / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _software.version / _struct_asym.entity_id / _struct_conf.beg_auth_asym_id / _struct_conf.end_auth_asym_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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.end_auth_asym_id
Description: Ligand geometry
Details: Very slight change to the orientation of the ligand in the active site.
Provider: author / Type: Coordinate replacement
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_validate_chiral / struct_conn
Item: _atom_site.label_alt_id / _chem_comp.formula ..._atom_site.label_alt_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: YD repeat-containing protein
A: YD repeat-containing protein
B: YD repeat-containing protein
C: YD repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,81610
Polymers71,0564
Non-polymers1,7606
Water75742
1
D: YD repeat-containing protein
hetero molecules

B: YD repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4635
Polymers35,5282
Non-polymers9353
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area2300 Å2
ΔGint-7 kcal/mol
Surface area11600 Å2
MethodPISA
2
A: YD repeat-containing protein
C: YD repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3535
Polymers35,5282
Non-polymers8253
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint1 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.570, 61.560, 87.780
Angle α, β, γ (deg.)90.00, 112.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
YD repeat-containing protein


Mass: 17763.900 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora maris AB-18-032 (bacteria)
Gene: VAB18032_16470 / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4F7G1
#2: Chemical ChemComp-8IF / (Z,2R,4S)-1-(4-methoxy-5-methylidene-2-oxidanylidene-furan-3-yl)-2,4-dimethyl-dodec-6-ene-1,5-dione


Mass: 348.433 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H28O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.58 Å3/Da / Density % sol: 52.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.02 M MgCl2, 0.1 M HEPES, 22% Polyacrylic acid sodium salt (MW 5100), pH 7.5

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.95→61.56 Å / Num. obs: 52793 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.989 / Rpim(I) all: 0.076 / Rrim(I) all: 0.189 / Net I/σ(I): 7.2
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 3710 / CC1/2: 0.293 / Rpim(I) all: 0.938

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DYV

5dyv


Resolution: 1.95→49.02 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.236 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24544 2553 4.8 %RANDOM
Rwork0.2177 ---
obs0.2191 50225 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.18 Å2
Baniso -1Baniso -2Baniso -3
1--2.3 Å20 Å20.94 Å2
2---2.76 Å20 Å2
3---3.14 Å2
Refinement stepCycle: 1 / Resolution: 1.95→49.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4287 0 0 42 4329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124380
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164131
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.8225950
X-RAY DIFFRACTIONr_angle_other_deg0.581.759471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8625535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.9387.21361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09210673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2659
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025250
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021030
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8884.862146
X-RAY DIFFRACTIONr_mcbond_other3.8864.862146
X-RAY DIFFRACTIONr_mcangle_it5.188.7082676
X-RAY DIFFRACTIONr_mcangle_other5.1798.7092677
X-RAY DIFFRACTIONr_scbond_it5.1045.4692234
X-RAY DIFFRACTIONr_scbond_other5.045.4612232
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5239.8153274
X-RAY DIFFRACTIONr_long_range_B_refined9.4648.414629
X-RAY DIFFRACTIONr_long_range_B_other9.46248.434628
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 187 -
Rwork0.399 3680 -
obs--99.9 %

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