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- PDB-6mkh: Crystal structure of pencillin binding protein 4 (PBP4) from Ente... -

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Basic information

Entry
Database: PDB / ID: 6mkh
TitleCrystal structure of pencillin binding protein 4 (PBP4) from Enterococcus faecalis in the imipenem-bound form
Componentspencillin binding protein 4 (PBP4)
Keywordsprotein binding/antibiotic / PBP / antibiotic / inhibitor / imipenem / PENICILLIN-BINDING PROTEIN / protein binding-antibiotic complex
Function / homology
Function and homology information


penicillin binding / response to antibiotic / 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
Chem-IM2 / PHOSPHATE ION / PBP4 protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pencillin binding protein 4 (PBP4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2004
Polymers70,7091
Non-polymers4913
Water1,45981
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)123.842, 85.401, 84.572
Angle α, β, γ (deg.)90.00, 110.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein pencillin 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-IM2 / (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carboxylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form / Imipenem


Mass: 301.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N3O4S / Comment: antibiotic*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.89 Å3/Da / Density % sol: 57.5 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2017
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: 2.62→37.895 Å / Num. obs: 77350 / % possible obs: 96 % / Redundancy: 4.6 % / Biso Wilson estimate: 48.35 Å2 / CC1/2: 0.959 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.047 / Rrim(I) all: 0.075 / Χ2: 0.72 / Net I/σ(I): 12.5
Reflection shellResolution: 2.62→2.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2364 / CC1/2: 0.321 / Rpim(I) all: 0.181 / Rrim(I) all: 0.28 / Χ2: 0.46 / % possible all: 77.3

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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: PBP4 apo

Resolution: 2.62→37.895 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 1244 5.2 %
Rwork0.1966 --
obs0.1986 23930 95.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.62→37.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3303 0 30 81 3414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033383
X-RAY DIFFRACTIONf_angle_d0.5694583
X-RAY DIFFRACTIONf_dihedral_angle_d12.9192027
X-RAY DIFFRACTIONf_chiral_restr0.044523
X-RAY DIFFRACTIONf_plane_restr0.004602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6196-2.72440.29971020.24111978X-RAY DIFFRACTION75
2.7244-2.84840.23361690.20742556X-RAY DIFFRACTION99
2.8484-2.99850.28181350.21032592X-RAY DIFFRACTION99
2.9985-3.18620.25281480.2012544X-RAY DIFFRACTION98
3.1862-3.43210.26311380.20362592X-RAY DIFFRACTION98
3.4321-3.77720.25591500.18422568X-RAY DIFFRACTION99
3.7772-4.32310.21121340.16652571X-RAY DIFFRACTION97
4.3231-5.44410.20661280.17562627X-RAY DIFFRACTION99
5.4441-37.89850.22681400.232658X-RAY DIFFRACTION98

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