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- PDB-6mki: Crystal structure of penicillin-binding protein 4 (PBP4) from Ent... -

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Basic information

Entry
Database: PDB / ID: 6mki
TitleCrystal structure of penicillin-binding protein 4 (PBP4) from Enterococcus faecalis in the ceftaroline-bound form
Componentspenicillin-binding protein 4 (PBP4)
Keywordsprotein binding/antibiotic / PBP / antibiotic / PENICILLIN-BINDING PROTEIN / protein binding-antibiotic complex
Function / homology
Function and homology information


penicillin binding / response to antibiotic / plasma membrane
Similarity search - Function
NTF2-like N-terminal transpeptidase / NTF2-like N-terminal transpeptidase domain / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / NTF2-like domain superfamily / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Ceftaroline, bound form / PHOSPHATE ION / PBP4 protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.984 Å
AuthorsD'Andrea, E.D. / Moon, T.M. / Peti, W. / Page, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI045626-15 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: The structures of penicillin-binding protein 4 (PBP4) and PBP5 fromEnterococciprovide structural insights into beta-lactam resistance.
Authors: Moon, T.M. / D'Andrea, E.D. / Lee, C.W. / Soares, A. / Jakoncic, J. / Desbonnet, C. / Garcia-Solache, M. / Rice, L.B. / Page, R. / Peti, W.
History
DepositionSep 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 3, 2024Group: 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: penicillin-binding protein 4 (PBP4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5995
Polymers70,7091
Non-polymers8904
Water46826
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)123.496, 85.572, 82.715
Angle α, β, γ (deg.)90.00, 109.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein penicillin-binding protein 4 (PBP4) / Penicillin-binding protein


Mass: 70709.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: pbp4, A6B47_10405, DAI13_12160 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K3C9
#2: Chemical ChemComp-AI8 / Ceftaroline, bound form


Mass: 607.729 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23N8O5S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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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: 2.77 Å3/Da / Density % sol: 55.64 % / Description: plate
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 3.25 / Details: 0.04M KH2PO4, 16% PEG 8000, 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2018
Details: Mirror: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.98→39.04 Å / Num. obs: 31379 / % possible obs: 97.5 % / Redundancy: 3.8 % / CC1/2: 0.89 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.113 / Rrim(I) all: 0.172 / Χ2: 0.74 / Net I/σ(I): 5.4
Reflection shellResolution: 2.98→3.17 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2468 / CC1/2: 0.881 / Rpim(I) all: 0.328 / Rrim(I) all: 0.492 / % possible all: 92.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimless0.6.3data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBP4 apo

Resolution: 2.984→39.038 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0.34 / Phase error: 30.12
RfactorNum. reflection% reflectionSelection details
Rfree0.2621 1595 5.09 %imported from PBP4 apo
Rwork0.225 ---
obs0.2269 31348 96.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.984→39.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3108 0 55 26 3189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023211
X-RAY DIFFRACTIONf_angle_d0.5554363
X-RAY DIFFRACTIONf_dihedral_angle_d12.41915
X-RAY DIFFRACTIONf_chiral_restr0.042497
X-RAY DIFFRACTIONf_plane_restr0.004575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9845-3.08080.32061280.28022351X-RAY DIFFRACTION85
3.0808-3.19080.25911660.25392727X-RAY DIFFRACTION99
3.1908-3.31850.33981210.24452793X-RAY DIFFRACTION98
3.3185-3.46950.26981630.2252701X-RAY DIFFRACTION98
3.4695-3.65230.31681550.21842694X-RAY DIFFRACTION96
3.6523-3.88090.30581500.21422690X-RAY DIFFRACTION97
3.8809-4.18020.25281660.18772753X-RAY DIFFRACTION99
4.1802-4.60030.18371020.18342824X-RAY DIFFRACTION99
4.6003-5.26460.23751560.20622742X-RAY DIFFRACTION98
5.2646-6.62760.25711400.25262721X-RAY DIFFRACTION98
6.6276-39.04140.24261480.25682757X-RAY DIFFRACTION98

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