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- PDB-6o6e: Crystal structure of PltF trapped with PltL using a proline adeno... -

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Entry
Database: PDB / ID: 6o6e
TitleCrystal structure of PltF trapped with PltL using a proline adenosine vinylsulfonamide inhibitor
Components
  • L-proline--[L-prolyl-carrier protein] ligase
  • Peptidyl carrier protein PltL
KeywordsLigase/Transport protein / nonribosomal peptide synthetase / NRPS / type II / biosynthesis / pyoluteorin / Ligase-Transport protein complex
Function / homology
Function and homology information


L-proline-[L-prolyl-carrier protein] ligase / amino acid activation for nonribosomal peptide biosynthetic process / peptide transport / secondary metabolite biosynthetic process / ligase activity / phosphopantetheine binding / antibiotic biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
AMP-binding / ANL, C-terminal domain / Amino acid adenylation domain / ACP-like / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A ...AMP-binding / ANL, C-terminal domain / Amino acid adenylation domain / ACP-like / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / ACP-like superfamily / Phosphopantetheine binding ACP domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Chem-I5M / MALONIC ACID / L-proline--[L-prolyl-carrier protein] ligase / Peptidyl carrier protein PltL
Similarity search - Component
Biological speciesPseudomonas protegens Pf-5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsCorpuz, J.C. / Podust, L.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)T32 GM008326 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM095970 United States
CitationJournal: Rsc Chem Biol / Year: 2020
Title: Dynamic visualization of type II peptidyl carrier protein recognition in pyoluteorin biosynthesis.
Authors: Corpuz, J.C. / Podust, L.M. / Davis, T.D. / Jaremko, M.J. / Burkart, M.D.
History
DepositionMar 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.0Jul 22, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / computing / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / struct_keywords / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.pdbx_database_id_DOI / _citation.year ..._citation.pdbx_database_id_DOI / _citation.year / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly_prop.value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_percent_reflns_obs / _refine_hist.cycle_id / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_all / _reflns.observed_criterion_sigma_F / _reflns.pdbx_CC_half / _reflns.pdbx_CC_star / _reflns.pdbx_Rrim_I_all / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_CC_star / _reflns_shell.pdbx_Rrim_I_all / _reflns_shell.pdbx_redundancy / _struct_keywords.pdbx_keywords / _struct_keywords.text / _struct_ref.db_code / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Description: Sequence discrepancy / Details: Identity of residues 499-505 have been corrected. / Provider: author / Type: Coordinate replacement
Revision 2.1Nov 11, 2020Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.year
Revision 2.2Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 3.0Jul 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_src_gen / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_assembly_prop / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_conf / struct_conn / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_ligand_of_interest / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_assembly_prop.value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[2][2] / _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.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.percent_reflns_obs / _reflns.d_resolution_low / _software.version / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Ligand geometry
Details: The stereochemistry of the ligand of interest has been corrected.
Provider: author / Type: Coordinate replacement
Revision 3.1Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 3.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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
B: L-proline--[L-prolyl-carrier protein] ligase
E: Peptidyl carrier protein PltL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,23419
Polymers67,5392
Non-polymers1,69417
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-27 kcal/mol
Surface area23190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.550, 170.550, 64.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 2 molecules BE

#1: Protein L-proline--[L-prolyl-carrier protein] ligase / L-prolyl-AMP ligase


Mass: 56397.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas protegens Pf-5 (bacteria) / Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: pltF, PFL_2792 / Plasmid: pET37b / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q4KCY5, L-proline-[L-prolyl-carrier protein] ligase
#2: Protein Peptidyl carrier protein PltL


Mass: 11141.683 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas protegens Pf-5 (bacteria) / Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: pltL, PFL_2786 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q4KCZ1

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Non-polymers , 5 types, 121 molecules

#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#6: Chemical ChemComp-I5M / 5'-deoxy-5'-({(2S)-2-({2-[(N-{(2R)-4-[(dioxo-lambda~5~-phosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-beta-alanyl)amino]ethyl}sulfanyl)-2-[(2S)-pyrrolidin-2-yl]ethanesulfonyl}amino)adenosine


Mass: 765.796 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44N9O11PS2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 4.09 Å3/Da / Density % sol: 69.93 % / Description: hexagonal prism, approximately 50 um long
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.73 / Details: 0.1 M malonic acid pH 5.73, 3.18 M sodium formate

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Data collection

DiffractionMean temperature: 110 K / Ambient temp details: liquid nitrogen stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 14, 2018 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.14→85.42 Å / Num. obs: 59600 / % possible obs: 99.2 % / Redundancy: 10.03 % / Biso Wilson estimate: 59.78 Å2 / CC1/2: 0.998 / CC star: 1 / Rrim(I) all: 0.2803 / Net I/σ(I): 9.73
Reflection shellResolution: 2.14→2.19 Å / Redundancy: 8.48 % / Mean I/σ(I) obs: 0.31 / Num. unique obs: 5360 / CC1/2: 0.0817 / CC star: 0.389 / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSJanuary 26, 2018data reduction
XDSJanuary 26, 2018data scaling
MOLREP11.2.08phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E7W

3e7w


Resolution: 2.14→85.42 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.97 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2601 2860 4.9 %RANDOM
Rwork0.2142 ---
obs0.2165 55991 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 148.68 Å2 / Biso mean: 58.52 Å2 / Biso min: 35.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 2.14→85.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4337 0 111 104 4552
Biso mean--67.39 59.95 -
Num. residues----578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134516
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174219
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.6536126
X-RAY DIFFRACTIONr_angle_other_deg1.2891.5899696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1585573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05921.315213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.14515694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0141534
X-RAY DIFFRACTIONr_chiral_restr0.0860.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025078
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02935
LS refinement shellResolution: 2.145→2.2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.47 198 -
Rwork0.483 3998 -
all-4196 -
obs--96.64 %

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