[English] 日本語
- PDB-6i1i: Crystal structure of TP domain from Escherichia coli penicillin-b... -

Open data

ID or keywords:


Basic information

Database: PDB / ID: 6i1i
TitleCrystal structure of TP domain from Escherichia coli penicillin-binding protein 3 in complex with penicillin
ComponentsPeptidoglycan D,D-transpeptidase FtsI,Peptidoglycan D,D-transpeptidase FtsI
KeywordsPEPTIDE BINDING PROTEIN / penicillin-binding protein / peptidoglycan / Transpeptidase
Function / homology
Function and homology information

peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / plasma membrane => GO:0005886
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Piperacillin (Open Form) / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (unknown)
AuthorsBellini, D. / Koekemoer, L. / Newman, H. / Dowson, C.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)grant.MR/P007503/1 United Kingdom
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Novel and Improved Crystal Structures of H. influenzae, E. coli and P. aeruginosa Penicillin-Binding Protein 3 (PBP3) and N. gonorrhoeae PBP2: Toward a Better Understanding of beta-Lactam ...Title: Novel and Improved Crystal Structures of H. influenzae, E. coli and P. aeruginosa Penicillin-Binding Protein 3 (PBP3) and N. gonorrhoeae PBP2: Toward a Better Understanding of beta-Lactam Target-Mediated Resistance.
Authors: Bellini, D. / Koekemoer, L. / Newman, H. / Dowson, C.G.
DepositionOct 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

Structure visualization

Structure viewerMolecule:

Downloads & links


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

Theoretical massNumber of molelcules
Total (without water)37,6492

  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13780 Å2
Unit cell
Length a, b, c (Å)99.714, 147.672, 43.254
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions





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

Mass: 37129.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (unknown) / Gene: ftsI, pbpB, Z0094, ECs0088 / Production host: Escherichia coli BL21(DE3) (unknown)
References: UniProt: P0AD69, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-JPP / Piperacillin (Open Form)

Mass: 519.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H29N5O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

Experimental details


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

Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 6,000, 0.1 M CaCl2, 15% ethylene glycol and 0.1 M TrisHCl pH 9

Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→43.25 Å / Num. obs: 32743 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rrim(I) all: 0.204 / Net I/σ(I): 6.8
Reflection shellResolution: 1.75→1.78 Å


DIALSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BJP
Resolution: 1.75→43.25 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.286 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24704 1701 5.2 %RANDOM
Rwork0.22015 ---
obs0.22155 31015 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.349 Å2
Baniso -1Baniso -2Baniso -3
1-2.9 Å20 Å20 Å2
2---0.88 Å2-0 Å2
3----2.03 Å2
Refinement stepCycle: 1 / Resolution: 1.75→43.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2458 0 0 76 2534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192515
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9963421
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7185323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86122.76694
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70615409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9181521
X-RAY DIFFRACTIONr_chiral_restr0.10.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211894
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 117 -
Rwork0.342 2066 -
obs--98.33 %

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