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- PDB-6xcq: Erythromycin esterase EreC, mutant H289N in its closed conformation -

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Basic information

Entry
Database: PDB / ID: 6xcq
TitleErythromycin esterase EreC, mutant H289N in its closed conformation
ComponentsEreC
KeywordsHYDROLASE / Macrolide / esterase
Function / homologyErythromycin esterase, proteobacteria / Erythromycin esterase / Erythromycin esterase / response to antibiotic / S-1,2-PROPANEDIOL / EreC
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZielinski, M. / Park, J. / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EreC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3852
Polymers48,3091
Non-polymers761
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.366, 92.678, 125.795
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-812-

HOH

21A-912-

HOH

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Components

#1: Protein EreC / Erythromycin esterase


Mass: 48308.895 Da / Num. of mol.: 1 / Mutation: H289N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ereC / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: C7C425
#2: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M phosphate-citrate pH 4.2, 5% (w/v) PEG 3000, 25% (v/v) 1,2-propanediol, 10% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.3418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Nov 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3418 Å / Relative weight: 1
ReflectionResolution: 2→28.152 Å / Num. obs: 27238 / % possible obs: 99.2 % / Redundancy: 2 % / CC1/2: 0.985 / Rmerge(I) obs: 0.03177 / Net I/σ(I): 35.24
Reflection shellResolution: 2→2.072 Å / Mean I/σ(I) obs: 8.61 / Num. unique obs: 2699 / CC1/2: 0.981 / CC star: 0.995

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Processing

Software
NameVersionClassification
PHENIX1.15.1_3469refinement
PROTEUM PLUSdata scaling
PDB_EXTRACT3.25data extraction
PROTEUM PLUSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B55

3b55


Resolution: 2→28.15 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2149 1992 -
Rwork0.1706 --
obs-27161 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→28.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 5 257 3401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073400
X-RAY DIFFRACTIONf_angle_d0.8814642
X-RAY DIFFRACTIONf_dihedral_angle_d11.5962779
X-RAY DIFFRACTIONf_chiral_restr0.052536
X-RAY DIFFRACTIONf_plane_restr0.006614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.02540.27681380.21691744X-RAY DIFFRACTION99
2.0254-2.0520.2751480.20511837X-RAY DIFFRACTION100
2.052-2.08010.26161420.18981777X-RAY DIFFRACTION100
2.0801-2.10980.29231420.18331781X-RAY DIFFRACTION100
2.1098-2.14130.22911440.1811802X-RAY DIFFRACTION100
2.1413-2.17480.24741340.17311728X-RAY DIFFRACTION100
2.1748-2.21040.26451480.17441851X-RAY DIFFRACTION100
2.2104-2.24850.23171370.18751742X-RAY DIFFRACTION100
2.2485-2.28940.2731280.25411585X-RAY DIFFRACTION89
2.2894-2.33340.27241320.23851669X-RAY DIFFRACTION93
2.3334-2.3810.3141420.19651780X-RAY DIFFRACTION100
2.381-2.43270.20351420.18321798X-RAY DIFFRACTION100
2.4327-2.48930.231380.18511702X-RAY DIFFRACTION96
2.4893-2.55150.25411170.21981508X-RAY DIFFRACTION83
2.5515-2.62040.29121400.17931799X-RAY DIFFRACTION100
2.6204-2.69750.20891430.17251765X-RAY DIFFRACTION100
2.6975-2.78450.19911360.171765X-RAY DIFFRACTION99
2.7845-2.88390.23231450.16051819X-RAY DIFFRACTION99
2.8839-2.99920.26221420.17021773X-RAY DIFFRACTION100
2.9992-3.13560.22751400.16961787X-RAY DIFFRACTION100
3.1356-3.30060.28261260.17021652X-RAY DIFFRACTION92
3.3006-3.50710.17491370.15091778X-RAY DIFFRACTION100
3.5071-3.77730.17571450.13761801X-RAY DIFFRACTION100
3.7773-4.15630.15581450.12691793X-RAY DIFFRACTION100
4.1563-4.75530.16511430.12231788X-RAY DIFFRACTION100
4.7553-5.98170.21051410.16251785X-RAY DIFFRACTION100
5.9817-28.150.17751490.17631796X-RAY DIFFRACTION100

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