[English] 日本語
Yorodumi
- PDB-8bit: Crystal structure of acyl-CoA synthetase from Metallosphaera sedu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bit
TitleCrystal structure of acyl-CoA synthetase from Metallosphaera sedula in complex with Coenzyme A and 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 / COENZYME A / 4-hydroxybutyrate--CoA ligase 1
Similarity search - Component
Biological speciesMetallosphaera sedula DSM 5348 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / pdbx_contact_author / 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_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _entity.formula_weight / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_strand_id / _entity_poly_seq.mon_id / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.auth_mon_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.end_auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_validate_peptide_omega.omega / _refine.B_iso_mean / _refine.aniso_B[1][1] / _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.ls_d_res_low / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R_Free / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _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.d_resolution_low / _reflns.pdbx_number_measured_all / _software.classification / _software.name / _software.version / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_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_class / _struct_conf.pdbx_PDB_helix_length / _struct_ref.pdbx_align_begin / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq_dif.pdbx_pdb_strand_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: Removed link between Lys256 and Cys299 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)132,7636
Polymers130,4492
Non-polymers2,3144
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)105.806, 93.190, 131.685
Angle α, β, γ (deg.)90.00, 91.12, 90.00
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 65224.586 Da / Num. of mol.: 2
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-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.: 2 / Source method: obtained synthetically / Formula: C12H16N5O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: Protein solution(~3 mg/ml) was mixed to a final volume of 1 uL in 1:1 ratio with reservoir solution containing 0.1M acetate pH 5.2, 0.2M NaCl, 6-8% PEG 1500.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.1→52.95 Å / Num. obs: 23358 / % possible obs: 99.9 % / Redundancy: 3.4 % / CC1/2: 0.981 / Rmerge(I) obs: 0.207 / Rpim(I) all: 0.132 / Rrim(I) all: 0.246 / Χ2: 0.95 / Net I/σ(I): 4.2
Reflection shellResolution: 3.1→3.31 Å / % possible obs: 99.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 1.132 / Num. measured all: 14154 / Num. unique obs: 4194 / CC1/2: 0.735 / Rpim(I) all: 0.728 / Rrim(I) all: 1.35 / Χ2: 0.98 / Net I/σ(I) obs: 1

-
Processing

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

3b7w


Resolution: 3.1→52.95 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.903 / SU B: 86.567 / SU ML: 0.608 / Cross valid method: THROUGHOUT / ESU R Free: 0.564 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27664 1249 5.4 %RANDOM
Rwork0.21032 ---
obs0.21387 22090 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.011 Å2
Baniso -1Baniso -2Baniso -3
1-3.21 Å2-0 Å21.21 Å2
2--0.17 Å20 Å2
3----3.42 Å2
Refinement stepCycle: 1 / Resolution: 3.1→52.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9039 0 148 0 9187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0129402
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168955
X-RAY DIFFRACTIONr_angle_refined_deg21.85412731
X-RAY DIFFRACTIONr_angle_other_deg0.6451.76820666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.83951122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.672574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.523101664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.21396
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210871
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022151
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_it4.4014.3284494
X-RAY DIFFRACTIONr_mcbond_other4.44.3284494
X-RAY DIFFRACTIONr_mcangle_it6.9247.7765614
X-RAY DIFFRACTIONr_mcangle_other6.9247.7765615
X-RAY DIFFRACTIONr_scbond_it5.2494.8184908
X-RAY DIFFRACTIONr_scbond_other5.2484.8194909
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.48.6867118
X-RAY DIFFRACTIONr_long_range_B_refined12.87954.1440546
X-RAY DIFFRACTIONr_long_range_B_other12.87954.1440547
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 88 -
Rwork0.385 1609 -
obs--99.65 %
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)
11.17820.1013-0.16360.9431-0.31132.34560.0095-0.1172-0.0124-0.12110.0284-0.1897-0.2160.6596-0.03790.27270.01740.12920.7762-0.0570.087925.798558.122918.0238
21.6002-0.1825-0.36451.1522-0.34183.63170.0653-0.0837-0.14310.13720.07580.1966-0.174-0.5866-0.14110.2320.16780.08720.41420.07290.06732.382414.226746.3235
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B8 - 602
2X-RAY DIFFRACTION2A8 - 602

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more