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- PDB-8biq: Crystal structure of acyl-COA synthetase from Metallosphaera sedu... -

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Basic information

Entry
Database: PDB / ID: 8biq
TitleCrystal structure of acyl-COA synthetase from Metallosphaera sedula in complex with acetyl-AMP
Components4-hydroxybutyrate--CoA ligase 1
KeywordsLIGASE / COA-ligase / acyl-COA ligase / acetyl-COA ligase / Thermostable ligase / Thermostable / Acetyl-AMP / substrate bound / monomer
Function / homology
Function and homology information


4-hydroxybutyrate-CoA ligase (AMP-forming) / medium-chain acyl-CoA ligase / : / propionate-CoA ligase / propionate-CoA ligase activity / medium-chain fatty acid-CoA ligase activity / acetate-CoA ligase / acetate-CoA ligase activity / fatty acid metabolic process / ATP binding / membrane
Similarity search - Function
ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme
Similarity search - Domain/homology
Chem-6R9 / ADENOSINE MONOPHOSPHATE / 4-hydroxybutyrate--CoA ligase 1
Similarity search - Component
Biological speciesMetallosphaera sedula DSM 5348 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCapra, N. / Thunnissen, A.M.W.H. / Janssen, D.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Front Catal / Year: 2024
Title: Adapting an acyl CoA ligase from Metallosphaera sedula for lactam formation by structure-guided protein engineering
Authors: Capra, N. / Lelievre, C. / Toure, O. / Fossey-Jouenne, A. / Vergne-Vaxelaire, C. / Janssen, D.B. / Thunnissen, A.M.W.H. / Zaparucha, A.
History
DepositionNov 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 2.0Feb 14, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / cell / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] ..._atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _cell.Z_PDB / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_atom_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_asym_id / _pdbx_struct_sheet_hbond.range_1_label_atom_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_atom_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_asym_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_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][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _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_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R_Free / _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.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _reflns.number_obs / _reflns.pdbx_CC_half / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_chi_squared / _reflns.pdbx_redundancy / _reflns_shell.Rmerge_I_obs / _reflns_shell.number_measured_all / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rrim_I_all / _reflns_shell.pdbx_chi_squared / _reflns_shell.pdbx_redundancy / _software.classification / _software.name / _software.version / _struct_asym.entity_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_sheet.number_strands / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sense / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id
Description: Atomic clashes
Details: Solved ligand-protein clashes, removed K256-C299 linkage.
Provider: author / Type: Coordinate replacement
Revision 2.1Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 4-hydroxybutyrate--CoA ligase 1
A: 4-hydroxybutyrate--CoA ligase 1
B: 4-hydroxybutyrate--CoA ligase 1
C: 4-hydroxybutyrate--CoA ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,3298
Polymers260,8984
Non-polymers1,4314
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.864, 88.289, 131.207
Angle α, β, γ (deg.)90.00, 92.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
4-hydroxybutyrate--CoA ligase 1 / Acetate--CoA ligase / Butyrate--CoA ligase / Propionate--CoA ligase


Mass: 65224.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Metallosphaera sedula DSM 5348 (archaea)
Strain: ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2 / Gene: Msed_0406 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CodonPlus RIPL
References: UniProt: A4YDT1, 4-hydroxybutyrate-CoA ligase (AMP-forming), acetate-CoA ligase, medium-chain acyl-CoA ligase, propionate-CoA ligase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-6R9 / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate


Mass: 389.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N5O8P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: Drops of 3 mg/ml protein solution dispensed with a Mosquito robot into MRC-SD2 plates containing commercial screens with different ratios (1.25:0.75, 0.75:1.25). Best crystals grown in 0.1M ...Details: Drops of 3 mg/ml protein solution dispensed with a Mosquito robot into MRC-SD2 plates containing commercial screens with different ratios (1.25:0.75, 0.75:1.25). Best crystals grown in 0.1M acetic acid pH 5.2, 200mM NaCl, 7-10% PEG3350. Crystals appeared after 24h.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→66.48 Å / Num. obs: 56843 / % possible obs: 99.7 % / Redundancy: 1.9 % / CC1/2: 0.962 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.165 / Rrim(I) all: 0.234 / Χ2: 0.79 / Net I/σ(I): 3.2
Reflection shellResolution: 2.8→2.88 Å / % possible obs: 99.9 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.817 / Num. measured all: 8336 / Num. unique obs: 4641 / CC1/2: 0.527 / Rpim(I) all: 0.817 / Rrim(I) all: 1.156 / Χ2: 0.79 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B7W

3b7w


Resolution: 2.8→66.48 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.886 / SU B: 64.626 / SU ML: 0.513 / Cross valid method: THROUGHOUT / ESU R Free: 0.451 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27325 2810 4.9 %RANDOM
Rwork0.23456 ---
obs0.23648 54003 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.627 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å2-0.47 Å2
2---1.28 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.8→66.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18032 0 95 0 18127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01218554
X-RAY DIFFRACTIONr_bond_other_d0.0010.01617735
X-RAY DIFFRACTIONr_angle_refined_deg2.0481.85325092
X-RAY DIFFRACTIONr_angle_other_deg0.6591.76940923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.70852233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.225137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.468103315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.22741
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0221575
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024289
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_it1.4811.2928947
X-RAY DIFFRACTIONr_mcbond_other1.4811.2928947
X-RAY DIFFRACTIONr_mcangle_it2.4572.3211175
X-RAY DIFFRACTIONr_mcangle_other2.4562.3211176
X-RAY DIFFRACTIONr_scbond_it1.7331.4399607
X-RAY DIFFRACTIONr_scbond_other1.7331.4399607
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9192.55813918
X-RAY DIFFRACTIONr_long_range_B_refined5.86515.4879230
X-RAY DIFFRACTIONr_long_range_B_other5.86515.4879231
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 201 -
Rwork0.367 3995 -
obs--99.81 %
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)
11.1917-0.1691-0.05650.3243-0.01672.88280.0291-0.1449-0.1121-0.00820.03520.1303-0.0419-0.1865-0.06420.29510.0176-0.01981.02820.03830.09443.0942-28.875245.9912
21.02840.0844-0.0590.7336-0.10641.5359-0.00230.0068-0.10870.0467-0.0220.01830.01990.03570.02430.17620.04320.02890.98890.00260.0169-1.032712.239318.0781
31.48680.1509-0.25210.7398-0.09052.18430.0649-0.14090.00450.030.00060.07870.0198-0.1487-0.06550.20050.02580.02581.01940.01360.0488-47.069720.288145.2829
41.7899-0.256-0.23771.6852-0.07792.152-0.04320.049-0.0746-0.1604-0.0944-0.1940.13580.07640.13770.29640.05840.06181.03740.03020.0694-50.5797-26.542318.9221
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D10 - 601
2X-RAY DIFFRACTION2A9 - 601
3X-RAY DIFFRACTION3B10 - 601
4X-RAY DIFFRACTION4C10 - 601

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