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

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Basic information

Entry
Database: PDB / ID: 6mkf
TitleCrystal structure of penicillin binding protein 5 (PBP5) from Enterococcus faecium in the imipenem-bound form
Componentspenicillin binding protein 5 (PBP5)
Keywordsprotein binding/antibiotic / transpeptidase / PBP / PENICILLIN-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; domain 1 / 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 ...NTF2-like; domain 1 / 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 / Nuclear Transport Factor 2; Chain: A, / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 / Derived calculations / Category: pdbx_audit_support / struct_conn
Item: _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.5Nov 20, 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)71,60117
Polymers69,8591
Non-polymers1,74216
Water2,954164
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)192.933, 192.933, 155.860
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: 69858.781 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-IM2 / (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form


Mass: 301.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N3O4S / Comment: antibiotic*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 6 Å3/Da / Density % sol: 79.5 % / Description: rod
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M trisodium citrate, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2016 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings
RadiationMonochromator: Double crystal cryo-cooled Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.8→29.84 Å / Num. obs: 42442 / % possible obs: 99.8 % / Redundancy: 18.3 % / Biso Wilson estimate: 66.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.052 / Rrim(I) all: 0.166 / Net I/σ(I): 20.1
Reflection shellResolution: 2.8→2.91 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.661 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4301 / CC1/2: 0.337 / Rpim(I) all: 0.678 / Rrim(I) all: 1.803 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBP5 apo open

Resolution: 2.8→29.84 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.29
RfactorNum. reflection% reflection
Rfree0.1985 2108 4.97 %
Rwork0.1727 --
obs0.174 42395 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4782 0 95 164 5041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024943
X-RAY DIFFRACTIONf_angle_d0.4946714
X-RAY DIFFRACTIONf_dihedral_angle_d16.4342970
X-RAY DIFFRACTIONf_chiral_restr0.04762
X-RAY DIFFRACTIONf_plane_restr0.003872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.86510.3311520.3242528X-RAY DIFFRACTION97
2.8651-2.93670.3541460.30212623X-RAY DIFFRACTION99
2.9367-3.0160.30651330.27112658X-RAY DIFFRACTION100
3.016-3.10470.28391730.26582623X-RAY DIFFRACTION100
3.1047-3.20480.29891460.26412625X-RAY DIFFRACTION100
3.2048-3.31920.24511460.21432656X-RAY DIFFRACTION100
3.3192-3.45190.25991260.20132683X-RAY DIFFRACTION100
3.4519-3.60870.21041410.17772660X-RAY DIFFRACTION100
3.6087-3.79860.19051310.1672682X-RAY DIFFRACTION100
3.7986-4.03610.19511190.1562701X-RAY DIFFRACTION100
4.0361-4.34690.19131450.13932692X-RAY DIFFRACTION100
4.3469-4.78270.14431330.13332720X-RAY DIFFRACTION100
4.7827-5.47110.15541500.13852713X-RAY DIFFRACTION100
5.4711-6.8790.16421260.16372788X-RAY DIFFRACTION100
6.879-29.84630.16411410.14712935X-RAY DIFFRACTION100

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