[English] 日本語
- PDB-6g0k: Crystal structure of Enterococcus faecium D63r Penicillin-Binding... -

Open data

ID or keywords:


Basic information

Database: PDB / ID: 6g0k
TitleCrystal structure of Enterococcus faecium D63r Penicillin-Binding protein 5 (PBP5fm)
ComponentsLow affinity penicillin-binding protein 5 (PBP5)
KeywordsANTIBIOTIC / penicillin-binding / ceftobiprole / Enterococcus faecium / Antibiotic resistance
Function / homology
Function and homology information

penicillin binding / response to antibiotic / membrane => GO:0016020 / plasma membrane
Similarity search - Function
NTF2-like N-terminal transpeptidase domain / NTF2-like N-terminal transpeptidase / 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
Low affinity penicillin-binding protein 5 (PBP5)
Similarity search - Component
Biological speciesEnterococcus faecium (unknown)
AuthorsSauvage, E. / El Gachi, M. / Herman, R. / Kerff, F. / Charlier, P.
CitationJournal: To Be Published
Title: Structural basis of inactivation of Enterococcus faecium penicillin binding protein 5 by ceftobiprole.
Authors: Sauvage, E. / El Gachi, M. / Kerff, F. / Herman, R. / Verlaine, O. / Amoroso, A. / Page, M.G.P. / Joris, B. / Charlier, P.
DepositionMar 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release

Structure visualization

Structure viewerMolecule:

Downloads & links


Deposited unit
A: Low affinity penicillin-binding protein 5 (PBP5)
B: Low affinity penicillin-binding protein 5 (PBP5)
C: Low affinity penicillin-binding protein 5 (PBP5)
hetero molecules

Theoretical massNumber of molelcules
Total (without water)214,24924

  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10680 Å2
ΔGint-227 kcal/mol
Surface area79890 Å2
Unit cell
Length a, b, c (Å)79.842, 128.852, 236.250
Angle α, β, γ (deg.)90.00, 93.88, 90.00
Int Tables number5
Space group name H-MC121


#1: Protein Low affinity penicillin-binding protein 5 (PBP5)

Mass: 70743.773 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (unknown) / Gene: pbp5 / Production host: Enterococcus faecium (unknown) / Strain (production host): D63r / References: UniProt: Q47759
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate

Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4

Experimental details


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

Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.97 %
Crystal growTemperature: 292 K / Method: evaporation
Details: Crystals were grown by the sitting-drop vapor diffusion method. Crystals were grown at 20C by mixing 1microL of PBP5fm (48 mg/ml), 2microL of reservoir (20% PEG8000 (w/v), 0.4 M Li2SO4 and ...Details: Crystals were grown by the sitting-drop vapor diffusion method. Crystals were grown at 20C by mixing 1microL of PBP5fm (48 mg/ml), 2microL of reservoir (20% PEG8000 (w/v), 0.4 M Li2SO4 and 100 mM Na acetate at pH 4.5) and 0.5 microL of 0.1M ceftobiprole (kind gift of Basilea Pharmaceutica. The crystal was cryoprotected in the same buffer containing 20 % (v/v) glycerol. Crystals were soaked for 5 min in 1 microl of 0.1 M ceftobiprole before cryoprotection.

Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.9→47.142 Å / Num. obs: 52908 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.095 / Rrim(I) all: 0.186 / Net I/σ(I): 8.5
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 7679 / Rpim(I) all: 0.481 / Rrim(I) all: 0.93 / % possible all: 100


PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→47.142 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.92
RfactorNum. reflection% reflection
Rfree0.2468 2689 5.08 %
Rwork0.1982 --
obs0.2007 52887 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→47.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14030 0 105 0 14135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01614312
X-RAY DIFFRACTIONf_angle_d1.419367
X-RAY DIFFRACTIONf_dihedral_angle_d10.9048681
X-RAY DIFFRACTIONf_chiral_restr0.0662178
X-RAY DIFFRACTIONf_plane_restr0.0092531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.95270.31591240.26422638X-RAY DIFFRACTION100
2.9527-3.00950.31531300.26592625X-RAY DIFFRACTION100
3.0095-3.07090.27941350.26052656X-RAY DIFFRACTION100
3.0709-3.13770.29541320.2512610X-RAY DIFFRACTION100
3.1377-3.21070.29091260.25542650X-RAY DIFFRACTION100
3.2107-3.2910.31311470.2552653X-RAY DIFFRACTION100
3.291-3.37990.28151500.24092590X-RAY DIFFRACTION100
3.3799-3.47930.28561410.22372682X-RAY DIFFRACTION100
3.4793-3.59160.2591430.21322620X-RAY DIFFRACTION100
3.5916-3.71990.26841300.20272598X-RAY DIFFRACTION100
3.7199-3.86880.22171540.19432650X-RAY DIFFRACTION100
3.8688-4.04480.23621550.18572607X-RAY DIFFRACTION100
4.0448-4.25790.21471410.16912657X-RAY DIFFRACTION100
4.2579-4.52450.22871430.15892655X-RAY DIFFRACTION100
4.5245-4.87350.21121720.15682590X-RAY DIFFRACTION100
4.8735-5.36330.19721450.16232680X-RAY DIFFRACTION100
5.3633-6.13790.21571390.18542654X-RAY DIFFRACTION100
6.1379-7.72760.26111410.18822656X-RAY DIFFRACTION100
7.7276-47.14790.23881410.18062727X-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