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- PDB-6mkg: Crystal structure of penicillin binding protein 5 (PBP5) from Ent... -

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Basic information

Entry
Database: PDB / ID: 6mkg
TitleCrystal structure of penicillin binding protein 5 (PBP5) from Enterococcus faecium in the benzylpenicilin-bound form
Componentspenicillin binding protein 5 (PBP5)
Keywordsprotein binding/antibiotic / transpeptidase / PBP5 / PEPTIDE BINDING PROTEIN / protein binding-antibiotic complex
Function / homology
Function and homology information


peptidoglycan L,D-transpeptidase activity / penicillin binding / cell wall organization / 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
OPEN FORM - PENICILLIN G / Pbp5
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsMoon, T.M. / Lee, C. / D'Andrea, E.D. / 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: penicillin binding protein 5 (PBP5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,27425
Polymers73,7281
Non-polymers2,54624
Water70339
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)192.315, 192.315, 156.094
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein penicillin binding protein 5 (PBP5)


Mass: 73728.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: pbp5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A075Q0W3
#2: Chemical ChemComp-PNM / OPEN FORM - PENICILLIN G


Mass: 336.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N2O4S
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
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: 5.65 Å3/Da / Density % sol: 78.23 % / Description: rod
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M trisodium citrate, 2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2016
Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.93→39.02 Å / Num. obs: 36859 / % possible obs: 99.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 57.8 Å2 / Rmerge(I) obs: 0.242 / Net I/σ(I): 9.2
Reflection shellResolution: 2.93→3.06 Å / Redundancy: 7.5 % / Rmerge(I) obs: 2.673 / Mean I/σ(I) obs: 1.7 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBP5 APO OPEN

Resolution: 2.94→39.02 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.74
RfactorNum. reflection% reflection
Rfree0.205 1784 4.88 %
Rwork0.192 --
obs0.192 36572 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.94→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4693 0 138 39 4870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024896
X-RAY DIFFRACTIONf_angle_d0.4536680
X-RAY DIFFRACTIONf_dihedral_angle_d13.932883
X-RAY DIFFRACTIONf_chiral_restr0.041758
X-RAY DIFFRACTIONf_plane_restr0.003868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9361-3.01540.32031170.30722483X-RAY DIFFRACTION93
3.0154-3.10410.30551740.28742600X-RAY DIFFRACTION100
3.1041-3.20430.30661480.2842625X-RAY DIFFRACTION100
3.2043-3.31870.24791360.25542638X-RAY DIFFRACTION100
3.3187-3.45150.27221300.23162657X-RAY DIFFRACTION100
3.4515-3.60850.21991420.20642652X-RAY DIFFRACTION100
3.6085-3.79860.18781250.19162681X-RAY DIFFRACTION100
3.7986-4.03640.19571200.17892684X-RAY DIFFRACTION100
4.0364-4.34770.18991440.15262674X-RAY DIFFRACTION100
4.3477-4.78450.14931360.14942699X-RAY DIFFRACTION100
4.7845-5.47520.17271450.16332713X-RAY DIFFRACTION100
5.4752-6.8920.19711250.18752776X-RAY DIFFRACTION100
6.892-39.02690.18321420.17052906X-RAY DIFFRACTION99

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