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

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Basic information

Entry
Database: PDB / ID: 6mka
TitleCrystal structure of penicillin binding protein 5 (PBP5) from Enterococcus faecium in the open conformation
Componentspenicillin binding protein 5 (PBP5)
KeywordsPROTEIN BINDING / transpeptidase / PBP
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: 2.698 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 1.4Oct 11, 2023Group: 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 5 (PBP5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,49218
Polymers69,8591
Non-polymers1,63317
Water2,252125
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)190.540, 190.540, 156.467
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 5.56 Å3/Da / Density % sol: 77.88 % / Description: rods
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: 2.7→39.5 Å / Num. obs: 45763 / % possible obs: 98.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 47.82 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.054 / Rrim(I) all: 0.08 / Net I/σ(I): 13
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4382 / CC1/2: 0.707 / Rpim(I) all: 0.419 / Rrim(I) all: 0.613 / % possible all: 97.6

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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: 5DVY

5dvy


Resolution: 2.698→39.503 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.206 2261 4.94 %
Rwork0.1793 --
obs0.1807 45727 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.698→39.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4664 0 85 125 4874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064806
X-RAY DIFFRACTIONf_angle_d0.7436549
X-RAY DIFFRACTIONf_dihedral_angle_d6.5572850
X-RAY DIFFRACTIONf_chiral_restr0.046757
X-RAY DIFFRACTIONf_plane_restr0.005847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6977-2.75630.3471390.29572611X-RAY DIFFRACTION96
2.7563-2.82040.32671320.272685X-RAY DIFFRACTION99
2.8204-2.89090.30521660.26132663X-RAY DIFFRACTION99
2.8909-2.9690.28461280.25032711X-RAY DIFFRACTION99
2.969-3.05640.29671640.24122617X-RAY DIFFRACTION97
3.0564-3.1550.29331600.24792657X-RAY DIFFRACTION99
3.155-3.26770.26091480.22332706X-RAY DIFFRACTION99
3.2677-3.39850.20441200.19362744X-RAY DIFFRACTION100
3.3985-3.5530.20571430.16822700X-RAY DIFFRACTION98
3.553-3.74020.19511410.15962702X-RAY DIFFRACTION98
3.7402-3.97440.19691200.15292734X-RAY DIFFRACTION99
3.9744-4.28090.18561420.13682733X-RAY DIFFRACTION100
4.2809-4.71110.13961370.13362749X-RAY DIFFRACTION98
4.7111-5.39130.15741520.14412748X-RAY DIFFRACTION98
5.3913-6.78690.18411300.18112814X-RAY DIFFRACTION99
6.7869-39.50750.17261390.17182892X-RAY DIFFRACTION96

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