[English] 日本語
- PDB-6bsq: Enterococcus faecalis Penicillin Binding Protein 4 (PBP4) -

Open data

ID or keywords:


Basic information

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 (unknown)
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.
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

Structure visualization

Structure viewerMolecule:

Downloads & links


Deposited unit
A: PBP4 protein
hetero molecules

Theoretical massNumber of molelcules
Total (without water)71,0006

  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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


#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 (unknown) / 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

Experimental details


ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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

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


SAINTdata reduction
SADABSdata scaling
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

About Yorodumi


Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more