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- PDB-6bsq: Enterococcus faecalis Penicillin Binding Protein 4 (PBP4) -

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Basic information

Entry
Database: PDB / ID: 6bsq
TitleEnterococcus faecalis Penicillin Binding Protein 4 (PBP4)
ComponentsPBP4 protein
KeywordsHYDROLASE / Penicillin binding protein / transpeptidase / beta-lactam / antibiotic
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 faecalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMoon, T.M. / 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)R56AI045626-15 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
DepositionDec 4, 2017Deposition 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 26, 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.identifier_ORCID / _citation_author.name
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 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 1.6Apr 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: PBP4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0006
Polymers70,7091
Non-polymers2915
Water10,827601
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)124.709, 84.625, 85.093
Angle α, β, γ (deg.)90.00, 109.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PBP4 protein / 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K3C9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 3 Å3/Da / Density % sol: 58.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 40 mM potassium phosphate monobasic, 18% PEG800, 22% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å
DetectorType: Bruker PHOTON II / Detector: CMOS / Date: Jul 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 1.8→17.512 Å / Num. obs: 76417 / % possible obs: 98.9 % / Redundancy: 6.7 % / Net I/σ(I): 16.5
Reflection shellResolution: 1.8→1.83 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBP5

Resolution: 1.8→17.512 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.14
RfactorNum. reflection% reflection
Rfree0.2167 3916 5.12 %
Rwork0.1914 --
obs0.1927 76417 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→17.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3580 0 15 601 4196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153698
X-RAY DIFFRACTIONf_angle_d1.1685019
X-RAY DIFFRACTIONf_dihedral_angle_d11.9422246
X-RAY DIFFRACTIONf_chiral_restr0.088575
X-RAY DIFFRACTIONf_plane_restr0.007659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82190.45921290.43192243X-RAY DIFFRACTION87
1.8219-1.8450.41911340.40292432X-RAY DIFFRACTION92
1.845-1.86920.35761250.37822486X-RAY DIFFRACTION96
1.8692-1.89480.41391290.33112519X-RAY DIFFRACTION97
1.8948-1.92180.28231250.27682600X-RAY DIFFRACTION99
1.9218-1.95050.25191300.23722623X-RAY DIFFRACTION100
1.9505-1.98090.23431470.20192634X-RAY DIFFRACTION100
1.9809-2.01340.21961440.17422561X-RAY DIFFRACTION100
2.0134-2.0480.20581410.17612605X-RAY DIFFRACTION100
2.048-2.08520.20321750.18182587X-RAY DIFFRACTION100
2.0852-2.12520.17481250.17432602X-RAY DIFFRACTION100
2.1252-2.16860.20691700.16932592X-RAY DIFFRACTION100
2.1686-2.21560.2031340.17512634X-RAY DIFFRACTION100
2.2156-2.26710.2141390.17542582X-RAY DIFFRACTION100
2.2671-2.32360.20781360.16942611X-RAY DIFFRACTION100
2.3236-2.38630.19971250.16382610X-RAY DIFFRACTION100
2.3863-2.45630.21121270.16582652X-RAY DIFFRACTION100
2.4563-2.53540.2041500.15992612X-RAY DIFFRACTION100
2.5354-2.62570.19291490.16772623X-RAY DIFFRACTION100
2.6257-2.73050.1811300.16612619X-RAY DIFFRACTION100
2.7305-2.85420.19181640.17172599X-RAY DIFFRACTION100
2.8542-3.0040.22141370.17712629X-RAY DIFFRACTION100
3.004-3.19120.19421570.16832578X-RAY DIFFRACTION100
3.1912-3.43590.19131340.16352658X-RAY DIFFRACTION100
3.4359-3.77850.18021490.15562616X-RAY DIFFRACTION100
3.7785-4.31810.16961430.1472621X-RAY DIFFRACTION100
4.3181-5.41350.1541280.15952679X-RAY DIFFRACTION100
5.4135-17.51250.23831400.21632694X-RAY DIFFRACTION100

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