[English] 日本語
Yorodumi
- PDB-7bn9: Crystal Structure of Bacillus subtilis Penicillin Binding Protein 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bn9
TitleCrystal Structure of Bacillus subtilis Penicillin Binding Protein 3
ComponentsPenicillin-binding protein 3
KeywordsHYDROLASE / Transpeptidase / penicillin-binding protein / low-affinity / peptidoglycan
Function / homology
Function and homology information


peptidoglycan L,D-transpeptidase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / plasma membrane => GO:0005886
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 domain / Penicillin-binding protein, transpeptidase / NTF2-like domain superfamily / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Penicillin-binding protein 3
Similarity search - Component
Biological speciesBacillus subtilis (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsRao, V.A. / Lewis, R.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N002679/1 United Kingdom
CitationJournal: To Be Published
Title: Cooperation between peptidoglycan transpeptidases and SEDS proteins in Bacillus subtilis cell division
Authors: Sassine, J. / Rao, V.A. / Goldsmith, G. / Breukink, E. / Lewis, R.J. / Daniel, R.A. / Vollmer, W.
History
DepositionJan 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Penicillin-binding protein 3
B: Penicillin-binding protein 3


Theoretical massNumber of molelcules
Total (without water)148,0412
Polymers148,0412
Non-polymers00
Water1,76598
1
A: Penicillin-binding protein 3


Theoretical massNumber of molelcules
Total (without water)74,0201
Polymers74,0201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein 3


Theoretical massNumber of molelcules
Total (without water)74,0201
Polymers74,0201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.624, 108.684, 238.691
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Penicillin-binding protein 3 / PBP 3 / PSPB20 / Penicillin-binding protein C


Mass: 74020.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (unknown)
Strain: 168 / Gene: pbpC, ycsM, yzsA, BSU04140
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (unknown)
References: UniProt: P42971, serine-type D-Ala-D-Ala carboxypeptidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM HEPES, pH 7.0, 20 % (w/v) PEG 6000, 200 mM NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.65→49.46 Å / Num. obs: 42319 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 59.24 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.7
Reflection shellResolution: 2.65→9.92 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4375 / CC1/2: 0.639 / % possible all: 100

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VQQ, 3EQU
Resolution: 2.65→49.46 Å / SU ML: 0.3984 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9362
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.269 2165 5.12 %
Rwork0.213 40154 -
obs0.2159 42319 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.61 Å2
Refinement stepCycle: LAST / Resolution: 2.65→49.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9181 0 0 98 9279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039353
X-RAY DIFFRACTIONf_angle_d0.696412670
X-RAY DIFFRACTIONf_chiral_restr0.04791414
X-RAY DIFFRACTIONf_plane_restr0.00451640
X-RAY DIFFRACTIONf_dihedral_angle_d5.8781270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.710.37731230.30682651X-RAY DIFFRACTION99.96
2.71-2.780.35951330.27872619X-RAY DIFFRACTION99.96
2.78-2.850.3261430.2772650X-RAY DIFFRACTION100
2.85-2.940.37681320.27452612X-RAY DIFFRACTION100
2.94-3.030.36251310.26692692X-RAY DIFFRACTION100
3.03-3.140.36551470.26562598X-RAY DIFFRACTION99.96
3.14-3.270.3171460.26762666X-RAY DIFFRACTION100
3.27-3.420.30441470.23832672X-RAY DIFFRACTION100
3.42-3.60.31171520.23012639X-RAY DIFFRACTION100
3.6-3.820.26111420.21062651X-RAY DIFFRACTION100
3.82-4.120.25331420.1872674X-RAY DIFFRACTION100
4.12-4.530.21641580.16772714X-RAY DIFFRACTION100
4.53-5.190.21791530.17462682X-RAY DIFFRACTION100
5.19-6.530.2481610.21182730X-RAY DIFFRACTION100
6.53-49.460.23431550.19052904X-RAY DIFFRACTION99.97

+
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