[English] 日本語
Yorodumi
- PDB-9fze: Pseudomonas aeruginosa penicillin binding protein 3 in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fze
TitlePseudomonas aeruginosa penicillin binding protein 3 in complex with meropenem
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsHYDROLASE / Transpeptidase / penicillin binding protein 3 / PBP3
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / 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-MER / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSmith, H.G. / Allen, M.D. / Basak, S. / Aniebok, V. / Beech, M.J. / Alshref, F.M. / Farley, A.J.M. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: Chem Sci / Year: 2024
Title: Structural basis of Pseudomonas aeruginosa penicillin binding protein 3 inhibition by the siderophore-antibiotic cefiderocol.
Authors: Smith, H.G. / Basak, S. / Aniebok, V. / Beech, M.J. / Alshref, F.M. / Allen, M.D. / Farley, A.J.M. / Schofield, C.J.
History
DepositionJul 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
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)56,3932
Polymers56,0081
Non-polymers3851
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.697, 89.076, 83.452
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 56007.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Disordered residues are not modelled / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ftsI, pbpB, PA4418 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: G3XD46, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-MER / (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.26 Å3/Da / Density % sol: 45.67 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.01 M zinc chloride, 0.1 M MES pH 6.0, 20 % w/v PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.99763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99763 Å / Relative weight: 1
ReflectionResolution: 2.1→60.89 Å / Num. obs: 56238 / % possible obs: 100 % / Redundancy: 10.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.055 / Net I/σ(I): 9
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 1.246 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2486 / CC1/2: 0.782 / Rpim(I) all: 0.398 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→44.54 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 27.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2539 2849 5.07 %
Rwork0.2127 --
obs0.2147 56238 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3842 0 0 344 4186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.494
X-RAY DIFFRACTIONf_dihedral_angle_d10.3421488
X-RAY DIFFRACTIONf_chiral_restr0.043611
X-RAY DIFFRACTIONf_plane_restr0.004719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.33591200.28612773X-RAY DIFFRACTION100
2.14-2.180.31151420.28572708X-RAY DIFFRACTION100
2.18-2.210.3331370.31622240X-RAY DIFFRACTION98
2.22-2.260.56371390.44212100X-RAY DIFFRACTION86
2.26-2.310.40271510.35992526X-RAY DIFFRACTION93
2.31-2.370.3381460.25922765X-RAY DIFFRACTION100
2.37-2.430.35191640.26852660X-RAY DIFFRACTION100
2.43-2.490.30291370.2592749X-RAY DIFFRACTION100
2.49-2.560.28061420.2522718X-RAY DIFFRACTION100
2.56-2.650.3291390.22932782X-RAY DIFFRACTION100
2.65-2.740.23171370.22322735X-RAY DIFFRACTION100
2.74-2.850.24791640.2292733X-RAY DIFFRACTION100
2.85-2.980.25071150.22612782X-RAY DIFFRACTION100
2.98-3.140.20871360.2162703X-RAY DIFFRACTION100
3.14-3.330.23661470.20562742X-RAY DIFFRACTION100
3.33-3.590.22011750.19662726X-RAY DIFFRACTION100
3.59-3.950.21681150.18642735X-RAY DIFFRACTION100
3.95-4.520.21361260.15422775X-RAY DIFFRACTION100
4.53-5.70.19321440.15772731X-RAY DIFFRACTION100
5.7-44.540.19481730.16382706X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 11.8835 Å / Origin y: 23.6934 Å / Origin z: 1.7164 Å
111213212223313233
T0.2371 Å2-0.0034 Å20.032 Å2-0.2872 Å20.0163 Å2--0.2645 Å2
L0.1118 °2-0.2616 °2-0.0147 °2-2.1715 °20.3718 °2--0.3716 °2
S0.0116 Å °0.0259 Å °0.0809 Å °-0.0175 Å °-0.0287 Å °0.0375 Å °-0.0741 Å °-0.0262 Å °0.0178 Å °
Refinement TLS groupSelection details: chain A

+
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