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- PDB-6xcs: Erythromycin esterase mutant EreC H289N in its open conformation -

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Basic information

Entry
Database: PDB / ID: 6xcs
TitleErythromycin esterase mutant EreC H289N in its open conformation
ComponentsEreC
KeywordsHYDROLASE / Macrolide / esterase
Function / homologyErythromycin esterase, proteobacteria / Erythromycin esterase / : / Erythromycin esterase / response to antibiotic / EreC
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZielinski, M. / Berghuis, A.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-162365 Canada
CitationJournal: Nat Commun / Year: 2021
Title: Structural and functional insights into esterase-mediated macrolide resistance.
Authors: Zielinski, M. / Park, J. / Sleno, B. / Berghuis, A.M.
History
DepositionJun 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._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 1.2Oct 18, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 30, 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: EreC
B: EreC


Theoretical massNumber of molelcules
Total (without water)97,8372
Polymers97,8372
Non-polymers00
Water1,18966
1
A: EreC


Theoretical massNumber of molelcules
Total (without water)48,9191
Polymers48,9191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EreC


Theoretical massNumber of molelcules
Total (without water)48,9191
Polymers48,9191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.367, 74.214, 129.290
Angle α, β, γ (deg.)90.000, 96.498, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRASPASP(chain 'A' and (resid 11 through 15 or (resid 16...AA12 - 7132 - 91
12ALAALAILEILE(chain 'A' and (resid 11 through 15 or (resid 16...AA74 - 18294 - 202
13ALAALAGLYGLY(chain 'A' and (resid 11 through 15 or (resid 16...AA185 - 188205 - 208
14GLUGLUALAALA(chain 'A' and (resid 11 through 15 or (resid 16...AA191 - 198211 - 218
15GLYGLYARGARG(chain 'A' and (resid 11 through 15 or (resid 16...AA201 - 243221 - 263
16ARGARGSERSER(chain 'A' and (resid 11 through 15 or (resid 16...AA246 - 253266 - 273
17GLYGLYSERSER(chain 'A' and (resid 11 through 15 or (resid 16...AA256 - 263276 - 283
18ALAALAARGARG(chain 'A' and (resid 11 through 15 or (resid 16...AA266 - 271286 - 291
19VALVALPROPRO(chain 'A' and (resid 11 through 15 or (resid 16...AA273 - 294293 - 314
110PHEPHEVALVAL(chain 'A' and (resid 11 through 15 or (resid 16...AA297 - 304317 - 324
111GLYGLYPROPRO(chain 'A' and (resid 11 through 15 or (resid 16...AA307 - 331327 - 351
112GLNGLNASPASP(chain 'A' and (resid 11 through 15 or (resid 16...AA334 - 357354 - 377
113GLUGLUALAALA(chain 'A' and (resid 11 through 15 or (resid 16...AA360 - 379380 - 399
114LYSLYSLYSLYS(chain 'A' and (resid 11 through 15 or (resid 16...AA382 - 384402 - 404
115ARGARGVALVAL(chain 'A' and (resid 11 through 15 or (resid 16...AA387 - 416407 - 436
21THRTHRASPASP(chain 'B' and (resid 11 through 13 or (resid 14...BB12 - 7132 - 91
22ALAALAILEILE(chain 'B' and (resid 11 through 13 or (resid 14...BB74 - 18294 - 202
23ALAALAGLYGLY(chain 'B' and (resid 11 through 13 or (resid 14...BB185 - 188205 - 208
24GLUGLUALAALA(chain 'B' and (resid 11 through 13 or (resid 14...BB191 - 198211 - 218
25GLYGLYARGARG(chain 'B' and (resid 11 through 13 or (resid 14...BB201 - 243221 - 263
26ARGARGSERSER(chain 'B' and (resid 11 through 13 or (resid 14...BB246 - 253266 - 273
27GLYGLYSERSER(chain 'B' and (resid 11 through 13 or (resid 14...BB256 - 263276 - 283
28ALAALAARGARG(chain 'B' and (resid 11 through 13 or (resid 14...BB266 - 271286 - 291
29VALVALPROPRO(chain 'B' and (resid 11 through 13 or (resid 14...BB273 - 294293 - 314
210PHEPHEVALVAL(chain 'B' and (resid 11 through 13 or (resid 14...BB297 - 304317 - 324
211GLYGLYPROPRO(chain 'B' and (resid 11 through 13 or (resid 14...BB307 - 331327 - 351
212GLNGLNASPASP(chain 'B' and (resid 11 through 13 or (resid 14...BB334 - 357354 - 377
213GLUGLUALAALA(chain 'B' and (resid 11 through 13 or (resid 14...BB360 - 379380 - 399
214LYSLYSLYSLYS(chain 'B' and (resid 11 through 13 or (resid 14...BB382 - 384402 - 404
215ARGARGVALVAL(chain 'B' and (resid 11 through 13 or (resid 14...BB387 - 416407 - 436

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Components

#1: Protein EreC / Erythromycin esterase


Mass: 48918.527 Da / Num. of mol.: 2 / Mutation: H289N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ereC / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: C7C425
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate pH 4.5, 5% (w/v) PEG 1000, 50% (v/v) ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.03322 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 2.4→44.804 Å / Num. obs: 35225 / % possible obs: 99.52 % / Redundancy: 3.9 % / Biso Wilson estimate: 51.69 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1007 / Rpim(I) all: 0.05935 / Rrim(I) all: 0.1171 / Net I/σ(I): 13.22
Reflection shellResolution: 2.4→2.486 Å / Num. unique obs: 3479 / CC1/2: 0.682 / CC star: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.15.1_3469refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XCQ

6xcq


Resolution: 2.4→44.8 Å / SU ML: 0.3469 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.608
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2899 1697 4.83 %
Rwork0.2405 33418 -
obs0.2431 35115 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.47 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6069 0 0 66 6135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00876207
X-RAY DIFFRACTIONf_angle_d1.31818449
X-RAY DIFFRACTIONf_chiral_restr0.07891011
X-RAY DIFFRACTIONf_plane_restr0.0081099
X-RAY DIFFRACTIONf_dihedral_angle_d9.29315130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.470.49191320.41792739X-RAY DIFFRACTION98.46
2.47-2.550.44721150.36722779X-RAY DIFFRACTION99.08
2.55-2.640.43941460.34412774X-RAY DIFFRACTION99.46
2.64-2.750.35791370.31522791X-RAY DIFFRACTION99.49
2.75-2.870.33011330.29462766X-RAY DIFFRACTION99.52
2.87-3.020.3531400.26912765X-RAY DIFFRACTION99.59
3.02-3.210.31281430.25112777X-RAY DIFFRACTION99.79
3.21-3.460.33811350.2412782X-RAY DIFFRACTION99.83
3.46-3.810.28781490.23732792X-RAY DIFFRACTION99.83
3.81-4.360.26931770.20252765X-RAY DIFFRACTION99.97
4.36-5.490.23631510.21492829X-RAY DIFFRACTION100
5.49-44.80.24391390.20492859X-RAY DIFFRACTION99.63

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