[English] 日本語
Yorodumi
- PDB-8f3h: Crystal structure of Penicillin Binding Protein 5 (PBP5) S466 ins... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8f3h
TitleCrystal structure of Penicillin Binding Protein 5 (PBP5) S466 insertion variant apo form from Enterococcus faecium
ComponentsPenicillin binding protein 5
KeywordsANTIBIOTIC / Penicillin binding / antibiotic resistance / ANTIBIOTICS
Function / homology
Function and homology information


peptidoglycan L,D-transpeptidase activity / penicillin binding / cell wall organization / response to antibiotic / plasma membrane
Similarity search - Function
NTF2-like; domain 1 / 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 ...NTF2-like; domain 1 / 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 / Nuclear Transport Factor 2; Chain: A, / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Penicillin binding protein 5
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsD'Andrea, E.D. / Choy, M.S. / Schoenle, M.V. / Page, R. / Peti, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2023
Title: The Molecular Basis for Resistance of E. faecium PBP5 to beta-lactam Antibiotics
Authors: Hunashal, Y. / Kumar, G.S. / Choy, M.S. / Da Silva Santiago, A. / D'Andrea, E.D. / Schoenle, M.V. / Arthur, M. / Rice, L.B. / Page, R. / Peti, W.
History
DepositionNov 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Penicillin binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,31623
Polymers70,2031
Non-polymers2,11322
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)193.917, 193.917, 154.813
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

-
Components

#1: Protein Penicillin binding protein 5 / Penicillin-binding protein Pbp5


Mass: 70203.102 Da / Num. of mol.: 1 / Mutation: S466 insertion
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: G5CKR9
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.98 Å3/Da / Density % sol: 79.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris pH 8.0, 3.0 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.6→38.7 Å / Num. obs: 53112 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.974 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.041 / Rrim(I) all: 0.122 / Net I/σ(I): 18.9 / Num. measured all: 685252
Reflection shellResolution: 2.6→2.68 Å / % possible obs: 99.1 % / Redundancy: 13 % / Rmerge(I) obs: 1.823 / Num. measured all: 58801 / Num. unique obs: 4513 / CC1/2: 0.998 / Rpim(I) all: 0.532 / Rrim(I) all: 1.904 / Net I/σ(I) obs: 1.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.68 Å38.7 Å
Translation7.68 Å38.7 Å

-
Processing

Software
NameVersionClassification
PHENIX1.19.1-4122refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.8.1phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MKA

6mka


Resolution: 2.6→38.7 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2175 2443 4.89 %
Rwork0.1944 --
obs0.1955 49962 94.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4903 0 110 220 5233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025094
X-RAY DIFFRACTIONf_angle_d0.4796909
X-RAY DIFFRACTIONf_dihedral_angle_d14.3911876
X-RAY DIFFRACTIONf_chiral_restr0.041765
X-RAY DIFFRACTIONf_plane_restr0.003898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.650.42081400.36092913X-RAY DIFFRACTION99
2.65-2.710.30461470.3062907X-RAY DIFFRACTION100
2.71-2.770.29841030.2762054X-RAY DIFFRACTION73
2.78-2.840.2935780.28981772X-RAY DIFFRACTION64
2.84-2.920.36871300.30132000X-RAY DIFFRACTION69
2.92-30.35311480.31012920X-RAY DIFFRACTION100
3.01-3.10.32651780.29292913X-RAY DIFFRACTION100
3.1-3.210.34811670.25842912X-RAY DIFFRACTION100
3.21-3.340.26941600.23422937X-RAY DIFFRACTION100
3.34-3.490.26111410.21232960X-RAY DIFFRACTION100
3.49-3.680.21031570.2022948X-RAY DIFFRACTION100
3.68-3.910.2191390.17882984X-RAY DIFFRACTION100
3.91-4.210.17411430.15732993X-RAY DIFFRACTION100
4.21-4.630.16791460.1392999X-RAY DIFFRACTION100
4.63-5.30.14471630.14923006X-RAY DIFFRACTION100
5.3-6.670.17711520.16723066X-RAY DIFFRACTION100
6.67-38.70.17581510.16993235X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
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

-
Yorodumi

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