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

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Basic information

Entry
Database: PDB / ID: 6mkj
TitleCrystal structure of penicillin binding protein 5 (PBP5) from Enterococcus faecium in the closed conformation
Componentspenicillin binding protein 5 (PBP5)
KeywordsPROTEIN BINDING / transpeptidase / PBP / PEPTIDE BINDING PROTEIN / penicillin binding protein
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
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.864 Å
AuthorsMoon, T.M. / Soares, A. / D'Andrea, E.D. / Jaconcic, J. / 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 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: penicillin binding protein 5 (PBP5)


Theoretical massNumber of molelcules
Total (without water)69,8591
Polymers69,8591
Non-polymers00
Water905
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)62.660, 62.660, 371.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.53 Å3/Da / Density % sol: 51.3 % / Description: plate
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5
Details: BisTris, 15% PEG 3350, 15% PEG 400, 0.1 M sucrose, 0.1 M trehalose, 0.1 M glucose, 0.1 M galactose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.86→29.7 Å / Num. obs: 18280 / % possible obs: 99.1 % / Redundancy: 12.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.152 / Rrim(I) all: 0.158 / Net I/σ(I): 12.7
Reflection shellResolution: 2.86→2.94 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 3 / Num. unique obs: 1164 / CC1/2: 0.778 / Rrim(I) all: 0.604 / % possible all: 90.6

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Processing

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

Resolution: 2.864→29.7 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 25.47
RfactorNum. reflection% reflection
Rfree0.2755 1803 10.01 %
Rwork0.2247 --
obs0.2299 18016 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.864→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4473 0 0 5 4478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024542
X-RAY DIFFRACTIONf_angle_d0.4976192
X-RAY DIFFRACTIONf_dihedral_angle_d14.7982711
X-RAY DIFFRACTIONf_chiral_restr0.041727
X-RAY DIFFRACTIONf_plane_restr0.003824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8641-2.94150.34451210.29721090X-RAY DIFFRACTION91
2.9415-3.0280.36781350.2861213X-RAY DIFFRACTION100
3.028-3.12560.30221380.28321237X-RAY DIFFRACTION100
3.1256-3.23720.33491330.26691209X-RAY DIFFRACTION100
3.2372-3.36660.3371370.25161224X-RAY DIFFRACTION100
3.3666-3.51960.30921390.241251X-RAY DIFFRACTION100
3.5196-3.70480.27011390.2411249X-RAY DIFFRACTION100
3.7048-3.93650.27191360.21641226X-RAY DIFFRACTION100
3.9365-4.23960.24321390.19831253X-RAY DIFFRACTION100
4.2396-4.66480.24311400.18781258X-RAY DIFFRACTION100
4.6648-5.33640.23381410.20091279X-RAY DIFFRACTION100
5.3364-6.71050.31431460.22591308X-RAY DIFFRACTION100
6.7105-29.70930.23871590.21241416X-RAY DIFFRACTION100

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