[English] 日本語
Yorodumi
- PDB-7atw: Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7atw
TitleStructure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 3)
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsHYDROLASE / D / D-transpeptidase / boron-binding / divalency
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / FtsZ-dependent cytokinesis / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / plasma membrane
Similarity search - Function
Peptidoglycan D,D-transpeptidase FtsI / 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 / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-RZZ / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.44 Å
AuthorsNewman, H. / Bellini, B. / Dowson, C.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: J.Med.Chem. / Year: 2021
Title: High-Throughput Crystallography Reveals Boron-Containing Inhibitors of a Penicillin-Binding Protein with Di- and Tricovalent Binding Modes.
Authors: Newman, H. / Krajnc, A. / Bellini, D. / Eyermann, C.J. / Boyle, G.A. / Paterson, N.G. / McAuley, K.E. / Lesniak, R. / Gangar, M. / von Delft, F. / Brem, J. / Chibale, K. / Schofield, C.J. / Dowson, C.G.
History
DepositionNov 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidoglycan D,D-transpeptidase FtsI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4815
Polymers58,0271
Non-polymers4544
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-1 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.301, 82.240, 88.521
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Peptidoglycan D,D-transpeptidase FtsI / Penicillin-binding protein 3 / PBP-3


Mass: 58027.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: ftsI, pbpB, PA4418 / Plasmid: pET47b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G3XD46, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-RZZ / 1-Hydroxy-1,3-dihydro-2,1-benzoxaborole-6-carboxylic acid / 1-methyl-3H-2,1-benzoxaborole-6-carboxylic acid / 1-Hydroxy-1,3-dihydrobenzo[c][1,2]oxaborole-6-carboxylic acid / 5-Carboxybenzoboroxole / 2,1-Benzoxaborole-6-carboxylic acid, 1,3-dihydro-1-hydroxy-


Mass: 177.950 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7BO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 25%(w/v) polyethylene glycol 3350, 0.1M Bis-Tris propane, 1%(w/v) protamine sulphate, pH 6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2018 / Details: Mirrors
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.44→60.25 Å / Num. obs: 67984 / % possible obs: 95.7 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.018 / Rrim(I) all: 0.048 / Net I/σ(I): 18
Reflection shellResolution: 1.44→1.59 Å / Redundancy: 6 % / Rmerge(I) obs: 0.869 / Num. unique obs: 3399 / CC1/2: 0.702 / Rpim(I) all: 0.381 / Rrim(I) all: 0.952 / % possible all: 67.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSJan 26, 2018data reduction
Aimless0.7.1data scaling
PHASER2.8.3phasing
REFMAC5.8.0258refinement
PHENIX1.18.2-3874refinement
STARANISO1.10.15data processing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HZR

6hzr


Resolution: 1.44→60.25 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.082
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.201 3362 4.945 %
Rwork0.1407 64622 -
all0.144 --
obs-67984 73.53 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.327 Å2
Baniso -1Baniso -2Baniso -3
1--0.944 Å2-0 Å2-0 Å2
2---1.216 Å2-0 Å2
3---2.16 Å2
Refinement stepCycle: LAST / Resolution: 1.44→60.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3767 0 30 202 3999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133937
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173786
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.6485353
X-RAY DIFFRACTIONr_angle_other_deg1.4481.5778752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6675510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.4820.569211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5215662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.091540
X-RAY DIFFRACTIONr_chiral_restr0.1040.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024481
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02839
X-RAY DIFFRACTIONr_nbd_refined0.2160.2702
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.23470
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21898
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21805
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2160
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1480.216
X-RAY DIFFRACTIONr_nbd_other0.2160.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1110.216
X-RAY DIFFRACTIONr_mcbond_it4.9733.1681989
X-RAY DIFFRACTIONr_mcbond_other4.9561725.121988
X-RAY DIFFRACTIONr_mcangle_it5.8774.7372486
X-RAY DIFFRACTIONr_mcangle_other5.87622.3542487
X-RAY DIFFRACTIONr_scbond_it7.4673.951948
X-RAY DIFFRACTIONr_scbond_other7.46719.8911948
X-RAY DIFFRACTIONr_scangle_it8.7055.6382857
X-RAY DIFFRACTIONr_scangle_other8.70414.7952858
X-RAY DIFFRACTIONr_lrange_it8.47138.3684220
X-RAY DIFFRACTIONr_lrange_other8.44738.7464187
X-RAY DIFFRACTIONr_rigid_bond_restr6.53533937
LS refinement shellResolution: 1.44→1.48 Å
RfactorNum. reflection% reflection
Rfree0.26 16 -
Rwork0.307 296 -
obs--4.5977 %

+
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