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- PDB-6e6t: Dieckmann cyclase, NcmC, bound to cerulenin -

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Basic information

Entry
Database: PDB / ID: 6e6t
TitleDieckmann cyclase, NcmC, bound to cerulenin
ComponentsNcmC
KeywordsLYASE/ANTIBIOTIC / Dieckmann cyclase / off-loading / Dieckmann condensation / LYASE-ANTIBIOTIC complex
Function / homologyAlpha/Beta hydrolase fold / Chem-HVV / NcmC
Function and homology information
Biological speciesSaccharothrix syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCogan, D.P. / Nair, S.K.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Structural Basis for Enzymatic Off-Loading of Hybrid Polyketides by Dieckmann Condensation.
Authors: Cogan, D.P. / Ly, J. / Nair, S.K.
History
DepositionJul 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 2.0Aug 5, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Experimental preparation / Other / Refinement description / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / diffrn / diffrn_radiation / entity / exptl_crystal_grow / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns_shell / software / struct_conf / struct_conn / struct_keywords / struct_site / struct_site_gen
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] / _diffrn.pdbx_serial_crystal_experiment / _diffrn_radiation.monochromator / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _exptl_crystal_grow.pdbx_details / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _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 / _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[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.ls_number_reflns_R_work / _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_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_starting_model / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _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 / _reflns_shell.number_unique_obs / _software.name / _software.version / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_keywords.pdbx_keywords / _struct_keywords.text / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_num_residues
Description: Real space R-factor / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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
Revision 2.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Oct 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

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Assembly

Deposited unit
A: NcmC
B: NcmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2716
Polymers57,6292
Non-polymers6434
Water6,738374
1
A: NcmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1363
Polymers28,8141
Non-polymers3212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NcmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1363
Polymers28,8141
Non-polymers3212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.269, 80.269, 77.743
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein NcmC


Mass: 28814.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharothrix syringae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1X9WEN9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HVV / (4S,5R)-4,5-dihydroxy-5-[(3E,6E)-octa-3,6-dien-1-yl]pyrrolidin-2-one / cerulenin, bound form


Mass: 225.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antifungal, antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.8 M ammonium sulfate, 1.8% w/v PEG400, 4% v/v formamide, 0.1 M HEPES, pH 7.0, 3 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 4, 2016
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.6→80.27 Å / Num. obs: 64817 / % possible obs: 99.7 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 17.8
Reflection shellResolution: 1.6→1.605 Å / Rmerge(I) obs: 0.924 / Num. unique obs: 6221

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Processing

Software
NameVersionClassification
PHENIXdev_3908refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6E6Y

6e6y


Resolution: 1.6→45.84 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 3174 4.9 %RANDOM
Rwork0.1878 61593 --
obs0.1893 64767 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.47 Å2 / Biso mean: 23.6338 Å2 / Biso min: 7.7 Å2
Refinement stepCycle: final / Resolution: 1.6→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 42 374 4312
Biso mean--21.79 31.11 -
Num. residues----525
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.620.31721140.29092521263595
1.62-1.650.2961450.27662605275097
1.65-1.680.2451000.250427272827100
1.68-1.710.2793990.239726992798100
1.71-1.740.24811630.225726472810100
1.74-1.770.24711390.20826892828100
1.77-1.810.25981200.206927122832100
1.81-1.840.22221270.194926672794100
1.85-1.890.2221830.182126352818100
1.89-1.940.24121230.174826982821100
1.94-1.990.21331280.180226812809100
1.99-2.050.19751270.179126982825100
2.05-2.110.18591640.169926902854100
2.11-2.190.22031320.170226692801100
2.19-2.270.1971620.172626542816100
2.28-2.380.21211830.179626602843100
2.38-2.50.22691220.180226902812100
2.5-2.660.24191440.185726772821100
2.66-2.870.2261260.185427302856100
2.87-3.150.19111120.193727092821100
3.15-3.610.20731890.181226462835100
3.61-4.550.21891340.169927292863100
4.55-45.840.20611380.186527602898100

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